Ubuntu Manpage: bcftools - utilities for variant calling and manipulating VCFs and BCFs.

NAME

       bcftools - utilities for variant calling and manipulating VCFs and BCFs.

SYNOPSIS

       bcftools [--version|--version-only] [--help] [COMMAND] [OPTIONS]

DESCRIPTION

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format
(VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and
BCFs, both uncompressed and BGZF-compressed.

Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even
when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed
VCF and BCF and streams will work in most, but not all situations. In general, whenever
multiple VCFs are read simultaneously, they must be indexed and therefore also compressed.
(Note that files with non-standard index names can be accessed as e.g. "bcftools view -r
X:2928329 file.vcf.gz##idx##non-standard-index-name".)

BCFtools is designed to work on a stream. It regards an input file "-" as the standard
input (stdin) and outputs to the standard output (stdout). Several commands can thus be
combined with Unix pipes.

VERSION
This manual page was last updated 2023-02-21 and refers to bcftools git version 1.17.

BCF1
The BCF1 format output by versions of samtools <= 0.1.19 is not compatible with this
version of bcftools. To read BCF1 files one can use the view command from old versions of
bcftools packaged with samtools versions <= 0.1.19 to convert to VCF, which can then be
read by this version of bcftools.

samtools-0.1.19/bcftools/bcftools view file.bcf1 | bcftools view

VARIANT CALLING
See bcftools call for variant calling from the output of the samtools mpileup command. In
versions of samtools <= 0.1.19 calling was done with bcftools view. Users are now required
to choose between the old samtools calling model (-c/--consensus-caller) and the new
multiallelic calling model (-m/--multiallelic-caller). The multiallelic calling model is
recommended for most tasks.

LIST OF COMMANDS

For a full list of available commands, run bcftools without arguments. For a full list of
available options, run bcftools COMMAND without arguments.

• annotate .. edit VCF files, add or remove annotations

• call .. SNP/indel calling (former "view")

• cnv .. Copy Number Variation caller

• concat .. concatenate VCF/BCF files from the same set of samples

• consensus .. create consensus sequence by applying VCF variants

• convert .. convert VCF/BCF to other formats and back

• csq .. haplotype aware consequence caller

• filter .. filter VCF/BCF files using fixed thresholds

• gtcheck .. check sample concordance, detect sample swaps and contamination

• head .. view VCF/BCF file headers

• index .. index VCF/BCF

• isec .. intersections of VCF/BCF files

• merge .. merge VCF/BCF files files from non-overlapping sample sets

• mpileup .. multi-way pileup producing genotype likelihoods

• norm .. normalize indels

• plugin .. run user-defined plugin

• polysomy .. detect contaminations and whole-chromosome aberrations

• query .. transform VCF/BCF into user-defined formats

• reheader .. modify VCF/BCF header, change sample names

• roh .. identify runs of homo/auto-zygosity

• sort .. sort VCF/BCF files

• stats .. produce VCF/BCF stats (former vcfcheck)

• view .. subset, filter and convert VCF and BCF files

LIST OF SCRIPTS

       Some helper scripts are bundled with the bcftools code.

       •   plot-vcfstats  .. plots the output of stats

COMMANDS AND OPTIONS

Common Options
The following options are common to many bcftools commands. See usage for specific
commands to see if they apply.

FILE
Files can be both VCF or BCF, uncompressed or BGZF-compressed. The file "-" is
interpreted as standard input. Some tools may require tabix- or CSI-indexed files.

-c, --collapse snps|indels|both|all|some|none|id
Controls how to treat records with duplicate positions and defines compatible records
across multiple input files. Here by "compatible" we mean records which should be
considered as identical by the tools. For example, when performing line intersections,
the desire may be to consider as identical all sites with matching positions (bcftools
isec -c all), or only sites with matching variant type (bcftools isec -c snps -c
indels), or only sites with all alleles identical (bcftools isec -c none).

none
only records with identical REF and ALT alleles are compatible

some
only records where some subset of ALT alleles match are compatible

all
all records are compatible, regardless of whether the ALT alleles match or not. In
the case of records with the same position, only the first will be considered and
appear on output.

snps
any SNP records are compatible, regardless of whether the ALT alleles match or
not. For duplicate positions, only the first SNP record will be considered and
appear on output.

indels
all indel records are compatible, regardless of whether the REF and ALT alleles
match or not. For duplicate positions, only the first indel record will be
considered and appear on output.

both
abbreviation of "-c indels -c snps"

id
only records with identical ID column are compatible. Supported by bcftools merge
only.

-f, --apply-filters LIST
Skip sites where FILTER column does not contain any of the strings listed in LIST. For
example, to include only sites which have no filters set, use -f .,PASS.

--no-version
Do not append version and command line information to the output VCF header.

-o, --output FILE
When output consists of a single stream, write it to FILE rather than to standard
output, where it is written by default. The file type is determined automatically from
the file name suffix and in case a conflicting -O option is given, the file name
suffix takes precedence.

-O, --output-type b|u|z|v[0-9]
Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF
(v). Use the -Ou option when piping between bcftools subcommands to speed up
performance by removing unnecessary compression/decompression and VCF←→BCF conversion.
The compression level of the compressed formats (b and z) can be set by by appending a
number between 0-9.

-r, --regions chr|chr:pos|chr:beg-end|chr:beg-[,...]
Comma-separated list of regions, see also -R, --regions-file. Overlapping records are
matched even when the starting coordinate is outside of the region, unlike the -t/-T
options where only the POS coordinate is checked. Note that -r cannot be used in
combination with -R.

-R, --regions-file FILE
Regions can be specified either on command line or in a VCF, BED, or tab-delimited
file (the default). The columns of the tab-delimited file can contain either positions
(two-column format: CHROM, POS) or intervals (three-column format: CHROM, BEG, END),
but not both. Positions are 1-based and inclusive. The columns of the tab-delimited
BED file are also CHROM, POS and END (trailing columns are ignored), but coordinates
are 0-based, half-open. To indicate that a file be treated as BED rather than the
1-based tab-delimited file, the file must have the ".bed" or ".bed.gz" suffix
(case-insensitive). Uncompressed files are stored in memory, while bgzip-compressed
and tabix-indexed region files are streamed. Note that sequence names must match
exactly, "chr20" is not the same as "20". Also note that chromosome ordering in FILE
will be respected, the VCF will be processed in the order in which chromosomes first
appear in FILE. However, within chromosomes, the VCF will always be processed in
ascending genomic coordinate order no matter what order they appear in FILE. Note that
overlapping regions in FILE can result in duplicated out of order positions in the
output. This option requires indexed VCF/BCF files. Note that -R cannot be used in
combination with -r.

--regions-overlap pos|record|variant|0|1|2
This option controls how overlapping records are determined: set to pos or 0 if the
VCF record has to have POS inside a region (this corresponds to the default behavior
of -t/-T); set to record or 1 if also overlapping records with POS outside a region
should be included (this is the default behavior of -r/-R, and includes indels with
POS at the end of a region, which are technically outside the region); or set to
variant or 2 to include only true overlapping variation (compare the full VCF
representation "TA>T-" vs the true sequence variation "A>-").

-s, --samples [^]LIST
Comma-separated list of samples to include or exclude if prefixed with "^." (Note that
when multiple samples are to be excluded, the "^" prefix is still present only once,
e.g. "^SAMPLE1,SAMPLE2".) The sample order is updated to reflect that given on the
command line. Note that in general tags such as INFO/AC, INFO/AN, etc are not updated
to correspond to the subset samples. bcftools view is the exception where some tags
will be updated (unless the -I, --no-update option is used; see bcftools view
documentation). To use updated tags for the subset in another command one can pipe
from view into that command. For example:

bcftools view -Ou -s sample1,sample2 file.vcf | bcftools query -f %INFO/AC\t%INFO/AN\n

-S, --samples-file [^]FILE
File of sample names to include or exclude if prefixed with "^". One sample per line.
See also the note above for the -s, --samples option. The sample order is updated to
reflect that given in the input file. The command bcftools call accepts an optional
second column indicating ploidy (0, 1 or 2) or sex (as defined by --ploidy, for
example "F" or "M"), for example:

sample1 1
sample2 2
sample3 2

sample1 M
sample2 F
sample3 F

If the second column is not present, the sex "F" is assumed. With bcftools call -C trio,
PED file is expected. The program ignores the first column and the last indicates sex
(1=male, 2=female), for example:

ignored_column daughterA fatherA motherA 2
ignored_column sonB fatherB motherB 1

-t, --targets [^]chr|chr:pos|chr:from-to|chr:from-[,...]
Similar as -r, --regions, but the next position is accessed by streaming the whole
VCF/BCF rather than using the tbi/csi index. Both -r and -t options can be applied
simultaneously: -r uses the index to jump to a region and -t discards positions
which are not in the targets. Unlike -r, targets can be prefixed with "^" to request
logical complement. For example, "^X,Y,MT" indicates that sequences X, Y and MT should
be skipped. Yet another difference between the -t/-T and -r/-R is that -r/-R checks
for proper overlaps and considers both POS and the end position of an indel, while
-t/-T considers the POS coordinate only (by default; see also --regions-overlap and
--targets-overlap). Note that -t cannot be used in combination with -T.

-T, --targets-file [^]FILE
Same -t, --targets, but reads regions from a file. Note that -T cannot be used in
combination with -t.

With the call -C alleles command, third column of the targets file must be
comma-separated list of alleles, starting with the reference allele. Note that the
file must be compressed and indexed. Such a file can be easily created from a VCF
using:

bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz

--threads INT
Use multithreading with INT worker threads. The option is currently used only for the
compression of the output stream, only when --output-type is b or z. Default: 0.

bcftools annotate [OPTIONS] FILE
Add or remove annotations.

-a, --annotations file
Bgzip-compressed and tabix-indexed file with annotations. The file can be VCF, BED, or
a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and
TO), optional columns REF and ALT, and arbitrary number of annotation columns. BED
files are expected to have the ".bed" or ".bed.gz" suffix (case-insensitive),
otherwise a tab-delimited file is assumed. Note that in case of tab-delimited file,
the coordinates POS, FROM and TO are one-based and inclusive. When REF and ALT are
present, only matching VCF records will be annotated. If the END coordinate is present
in the annotation file and given on command line as "-c ~INFO/END", then VCF records
will be matched also by the INFO/END coordinate. If ID is present in the annotation
file and given as "-c ~ID", then VCF records will be matched also by the ID column.

When multiple ALT alleles are present in the annotation file (given as comma-separated
list of alleles), at least one must match one of the alleles in the corresponding VCF
record. Similarly, at least one alternate allele from a multi-allelic VCF record must
be present in the annotation file.

Missing values can be added by providing "." in place of actual value and using the
missing value modifier with -c, such as ".TAG".

Note that flag types, such as "INFO/FLAG", can be annotated by including a field with
the value "1" to set the flag, "0" to remove it, or "." to keep existing flags. See
also -c, --columns and -h, --header-lines.

# Sample annotation file with columns CHROM, POS, STRING_TAG, NUMERIC_TAG
1 752566 SomeString 5
1 798959 SomeOtherString 6

-c, --columns list
Comma-separated list of columns or tags to carry over from the annotation file (see
also -a, --annotations). If the annotation file is not a VCF/BCF, list describes the
columns of the annotation file and must include CHROM, POS (or, alternatively, FROM
and TO), and optionally REF and ALT. Unused columns which should be ignored can be
indicated by "-".

If the annotation file is a VCF/BCF, only the edited columns/tags must be present and
their order does not matter. The columns ID, QUAL, FILTER, INFO and FORMAT can be
edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG", and FORMAT
tags can be written as "FORMAT/TAG" or "FMT/TAG". The imported VCF annotations can be
renamed as "DST_TAG:=SRC_TAG" or "FMT/DST_TAG:=FMT/SRC_TAG".

To carry over all INFO annotations, use "INFO". To add all INFO annotations except
"TAG", use "^INFO/TAG". By default, existing values are replaced.

By default, existing tags are overwritten unless the source value is a missing value
(i.e. "."). If also missing values should be carried over (and overwrite existing
tags), use ".TAG" instead of "TAG". To add annotations without overwriting existing
values (that is, to add tags that are absent or to add values to existing tags with
missing values), use "+TAG" instead of "TAG". These can be combined, for example
".+TAG" can be used to add TAG even if the source value is missing but only if TAG
does not exist in the target file; existing tags will not be overwritten. To append to
existing values (rather than replacing or leaving untouched), use "=TAG" (instead of
"TAG" or "+TAG"). To replace only existing values without modifying missing
annotations, use "-TAG". To match the record also by ID or INFO/END, in addition to
REF and ALT, use "~ID" or "~INFO/END". If position needs to be replaced, mark the
column with the new position as "~POS".

If the annotation file is not a VCF/BCF, all new annotations must be defined via -h,
--header-lines.

See also the -l, --merge-logic option.

-C, --columns-file file
Read the list of columns from a file (normally given via the -c, --columns option).
"-" to skip a column of the annotation file. One column name per row, an additional
space- or tab-separated field can be present to indicate the merge logic (normally
given via the -l, --merge-logic option). This is useful when many annotations are
added at once.

-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

--force
continue even when parsing errors, such as undefined tags, are encountered. Note this
can be an unsafe operation and can result in corrupted BCF files. If this option is
used, make sure to sanity check the result thoroughly.

-h, --header-lines file
Lines to append to the VCF header, see also -c, --columns and -a, --annotations. For
example:

##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">

-I, --set-id [+]FORMAT
assign ID on the fly. The format is the same as in the query command (see below). By
default all existing IDs are replaced. If the format string is preceded by "+", only
missing IDs will be set. For example, one can use

bcftools annotate --set-id +'%CHROM\_%POS\_%REF\_%FIRST_ALT' file.vcf

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.

-k, --keep-sites
keep sites which do not pass -i and -e expressions instead of discarding them

-l, --merge-logic tag:first|append|append-missing|unique|sum|avg|min|max[,...]
When multiple regions overlap a single record, this option defines how to treat
multiple annotation values when setting tag in the destination file: use the first
encountered value ignoring the rest (first); append allowing duplicates (append);
append even if the appended value is missing, i.e. is a dot (append-missing); append
discarding duplicate values (unique); sum the values (sum, numeric fields only);
average the values (avg); use the minimum value (min) or the maximum (max). + Note
that this option is intended for use with BED or TAB-delimited annotation files only.
Moreover, it is effective only when either REF and ALT or BEG and END --columns are
present . + Multiple rules can be given either as a comma-separated list or giving the
option multiple times. This is an experimental feature.

-m, --mark-sites TAG
annotate sites which are present ("+") or absent ("-") in the -a file with a new
INFO/TAG flag

--min-overlap ANN:'VCF'
minimum overlap required as a fraction of the variant in the annotation -a file (ANN),
in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). By default
overlaps of arbitrary length are sufficient. The option can be used only with the
tab-delimited annotation -a file and with BEG and END columns present.

--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v[0-9]
see Common Options

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

--rename-annots file
rename annotations according to the map in file, with "old_name new_name\n" pairs
separated by whitespaces, each on a separate line. The old name must be prefixed with
the annotation type: INFO, FORMAT, or FILTER.

--rename-chrs file
rename chromosomes according to the map in file, with "old_name new_name\n" pairs
separated by whitespaces, each on a separate line.

-s, --samples [^]LIST
subset of samples to annotate, see also Common Options

-S, --samples-file FILE
subset of samples to annotate. If the samples are named differently in the target VCF
and the -a, --annotations VCF, the name mapping can be given as "src_name dst_name\n",
separated by whitespaces, each pair on a separate line.

--single-overlaps
use this option to keep memory requirements low with very large annotation files.
Note, however, that this comes at a cost, only single overlapping intervals are
considered in this mode. This was the default mode until the commit af6f0c9 (Feb 24
2019).

--threads INT
see Common Options

-x, --remove list
List of annotations to remove. Use "FILTER" to remove all filters or
"FILTER/SomeFilter" to remove a specific filter. Similarly, "INFO" can be used to
remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT. To remove all
INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT
and FILTER). "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".

Examples:

# Remove three fields
bcftools annotate -x ID,INFO/DP,FORMAT/DP file.vcf.gz

# Remove all INFO fields and all FORMAT fields except for GT and PL
bcftools annotate -x INFO,^FORMAT/GT,FORMAT/PL file.vcf

# Add ID, QUAL and INFO/TAG, not replacing TAG if already present
bcftools annotate -a src.bcf -c ID,QUAL,+TAG dst.bcf

# Carry over all INFO and FORMAT annotations except FORMAT/GT
bcftools annotate -a src.bcf -c INFO,^FORMAT/GT dst.bcf

# Annotate from a tab-delimited file with six columns (the fifth is ignored),
# first indexing with tabix. The coordinates are 1-based.
tabix -s1 -b2 -e2 annots.tab.gz
bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,POS,REF,ALT,-,TAG file.vcf

# Annotate from a tab-delimited file with regions (1-based coordinates, inclusive)
tabix -s1 -b2 -e3 annots.tab.gz
bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf

# Annotate from a bed file (0-based coordinates, half-closed, half-open intervals)
bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf

# Transfer the INFO/END tag, matching by POS,REF,ALT and ID. This example assumes
# that INFO/END is already present in the VCF header.
bcftools annotate -a annots.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END input.vcf

# For more examples see http://samtools.github.io/bcftools/howtos/annotate.html

bcftools call [OPTIONS] FILE
This command replaces the former bcftools view caller. Some of the original functionality
has been temporarily lost in the process of transition under htslib
<http://github.com/samtools/htslib>, but will be added back on popular demand. The
original calling model can be invoked with the -c option.

File format options:
--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v[0-9]
see Common Options

--ploidy ASSEMBLY[?]
predefined ploidy, use list (or any other unused word) to print a list of all
predefined assemblies. Append a question mark to print the actual definition. See also
--ploidy-file.

--ploidy-file FILE
ploidy definition given as a space/tab-delimited list of CHROM, FROM, TO, SEX, PLOIDY.
The SEX codes are arbitrary and correspond to the ones used by --samples-file. The
default ploidy can be given using the starred records (see below), unlisted regions
have ploidy 2. The default ploidy definition is

X 1 60000 M 1
X 2699521 154931043 M 1
Y 1 59373566 M 1
Y 1 59373566 F 0
MT 1 16569 M 1
MT 1 16569 F 1
* * * M 2
* * * F 2

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

-s, --samples LIST
see Common Options

-S, --samples-file FILE
see Common Options

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see Common Options

--targets-overlap 0|1|2
see Common Options

--threads INT
see Common Options

Input/output options:
-A, --keep-alts
output all alternate alleles present in the alignments even if they do not appear in
any of the genotypes

-f, --format-fields list
comma-separated list of FORMAT fields to output for each sample. Currently GQ and GP
fields are supported. For convenience, the fields can be given as lower case letters.
Prefixed with "^" indicates a request for tag removal of auxiliary tags useful only
for calling.

-F, --prior-freqs AN,AC
take advantage of prior knowledge of population allele frequencies. The workflow looks
like this:

# Extract AN,AC values from an existing VCF, such 1000Genomes
bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' 1000Genomes.bcf | bgzip -c > AFs.tab.gz

# If the tags AN,AC are not already present, use the +fill-tags plugin
bcftools +fill-tags 1000Genomes.bcf | bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' | bgzip -c > AFs.tab.gz
tabix -s1 -b2 -e2 AFs.tab.gz

# Create a VCF header description, here we name the tags REF_AN,REF_AC
cat AFs.hdr
##INFO=<ID=REF_AN,Number=1,Type=Integer,Description="Total number of alleles in reference genotypes">
##INFO=<ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele">

# Now before calling, stream the raw mpileup output through `bcftools annotate` to add the frequencies
bcftools mpileup [...] -Ou | bcftools annotate -a AFs.tab.gz -h AFs.hdr -c CHROM,POS,REF,ALT,REF_AN,REF_AC -Ou | bcftools call -mv -F REF_AN,REF_AC [...]

-G, --group-samples FILE|-
by default, all samples are assumed to come from a single population. This option
allows to group samples into populations and apply the HWE assumption within but not
across the populations. FILE is a tab-delimited text file with sample names in the
first column and group names in the second column. If - is given instead, no HWE
assumption is made at all and single-sample calling is performed. (Note that in low
coverage data this inflates the rate of false positives.) The -G option requires the
presence of per-sample FORMAT/QS or FORMAT/AD tag generated with bcftools mpileup -a
QS (or -a AD).

-g, --gvcf INT
output also gVCF blocks of homozygous REF calls. The parameter INT is the minimum
per-sample depth required to include a site in the non-variant block.

-i, --insert-missed INT
output also sites missed by mpileup but present in -T, --targets-file.

-M, --keep-masked-ref
output sites where REF allele is N

-V, --skip-variants snps|indels
skip indel/SNP sites

-v, --variants-only
output variant sites only

Consensus/variant calling options:
-c, --consensus-caller
the original samtools/bcftools calling method (conflicts with -m)

-C, --constrain alleles|trio

alleles
call genotypes given alleles. See also -T, --targets-file.

trio
call genotypes given the father-mother-child constraint. See also -s, --samples
and -n, --novel-rate.

-m, --multiallelic-caller
alternative model for multiallelic and rare-variant calling designed to overcome known
limitations in -c calling model (conflicts with -c)

-n, --novel-rate float[,...]
likelihood of novel mutation for constrained -C trio calling. The trio genotype
calling maximizes likelihood of a particular combination of genotypes for father,
mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn).
By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions
and insertions, respectively. If two values are given, the first is interpreted as the
mutation rate of SNPs and the second is used to calculate the mutation rate of indels
according to their length as Pn=float*exp(-a-b*len), where a=22.8689, b=0.2994 for
insertions and a=21.9313, b=0.2856 for deletions [pubmed:23975140]. If only one value
is given, the same mutation rate Pn is used for SNPs and indels.

-p, --pval-threshold float
with -c, accept variant if P(ref|D) < float.

-P, --prior float
expected substitution rate, or 0 to disable the prior. Only with -m.

-t, --targets file|chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-X, --chromosome-X
haploid output for male samples (requires PED file with -s)

-Y, --chromosome-Y
haploid output for males and skips females (requires PED file with -s)

bcftools cnv [OPTIONS] FILE
Copy number variation caller, requires a VCF annotated with the Illumina’s B-allele
frequency (BAF) and Log R Ratio intensity (LRR) values. The HMM considers the following
copy number states: CN 2 (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy
gain).

General Options:
-c, --control-sample string
optional control sample name. If given, pairwise calling is performed and the -P
option can be used

-f, --AF-file file
read allele frequencies from a tab-delimited file with the columns CHR,POS,REF,ALT,AF

-o, --output-dir path
output directory

-p, --plot-threshold float
call matplotlib to produce plots for chromosomes with quality at least float, useful
for visual inspection of the calls. With -p 0, plots for all chromosomes will be
generated. If not given, a matplotlib script will be created but not called.

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

-s, --query-sample string
query sample name

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see Common Options

--targets-overlap 0|1|2
see Common Options

HMM Options:
-a, --aberrant float[,float]
fraction of aberrant cells in query and control. The hallmark of duplications and
contaminations is the BAF value of heterozygous markers which is dependent on the
fraction of aberrant cells. Sensitivity to smaller fractions of cells can be increased
by setting -a to a lower value. Note however, that this comes at the cost of increased
false discovery rate.

-b, --BAF-weight float
relative contribution from BAF

-d, --BAF-dev float[,float]
expected BAF deviation in query and control, i.e. the noise observed in the data.

-e, --err-prob float
uniform error probability

-l, --LRR-weight float
relative contribution from LRR. With noisy data, this option can have big effect on
the number of calls produced. In truly random noise (such as in simulated data), the
value should be set high (1.0), but in the presence of systematic noise when LRR are
not informative, lower values result in cleaner calls (0.2).

-L, --LRR-smooth-win int
reduce LRR noise by applying moving average given this window size

-O, --optimize float
iteratively estimate the fraction of aberrant cells, down to the given fraction.
Lowering this value from the default 1.0 to say, 0.3, can help discover more events
but also increases noise

-P, --same-prob float
the prior probability of the query and the control sample being the same. Setting to 0
calls both independently, setting to 1 forces the same copy number state in both.

-x, --xy-prob float
the HMM probability of transition to another copy number state. Increasing this values
leads to smaller and more frequent calls.

bcftools concat [OPTIONS] FILE1 FILE2 [...]
Concatenate or combine VCF/BCF files. All source files must have the same sample columns
appearing in the same order. Can be used, for example, to concatenate chromosome VCFs into
one VCF, or combine a SNP VCF and an indel VCF into one. The input files must be sorted by
chr and position. The files must be given in the correct order to produce sorted VCF on
output unless the -a, --allow-overlaps option is specified. With the --naive option, the
files are concatenated without being recompressed, which is very fast..

-a, --allow-overlaps
First coordinate of the next file can precede last record of the current file.

-c, --compact-PS
Do not output PS tag at each site, only at the start of a new phase set block.

-d, --rm-dups snps|indels|both|all|exact
Output duplicate records of specified type present in multiple files only once. Note
that records duplicate within one file are not removed with this option, for that use
bcftools norm -d instead.
In other words, the default behavior of the program is similar to unix "cat" in that
when two files contain a record with the same position, that position will appear
twice on output. With -d, every line that finds a matching record in another file will
be printed only once.
Requires -a, --allow-overlaps.

-D, --remove-duplicates
Alias for -d exact

-f, --file-list FILE
Read file names from FILE, one file name per line.

-l, --ligate
Ligate phased VCFs by matching phase at overlapping haplotypes. Note that the option
is intended for VCFs with perfect overlap, sites in overlapping regions present in one
but missing in the other are dropped.

--ligate-force
Keep all sites and ligate even non-overlapping chunks and chunks with imperfect
overlap

--ligate-warn
Drop sites in imperfect overlaps

--no-version
see Common Options

-n, --naive
Concatenate VCF or BCF files without recompression. This is very fast but requires
that all files are of the same type (all VCF or all BCF) and have the same headers.
This is because all tags and chromosome names in the BCF body rely on the order of the
contig and tag definitions in the header. A header check compatibility is performed
and the program throws an error if it is not safe to use the option.

--naive-force
Same as --naive, but header compatibility is not checked. Dangerous, use with caution.

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v[0-9]
see Common Options

-q, --min-PQ INT
Break phase set if phasing quality is lower than INT

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options. Requires -a, --allow-overlaps.

-R, --regions-file FILE
see Common Options. Requires -a, --allow-overlaps.

--regions-overlap 0|1|2
see Common Options

--threads INT
see Common Options

bcftools consensus [OPTIONS] FILE
Create consensus sequence by applying VCF variants to a reference fasta file. By default,
the program will apply all ALT variants to the reference fasta to obtain the consensus
sequence. Using the --sample (and, optionally, --haplotype) option will apply genotype
(haplotype) calls from FORMAT/GT. Note that the program does not act as a primitive
variant caller and ignores allelic depth information, such as INFO/AD or FORMAT/AD. For
that, consider using the setGT plugin.

-a, --absent CHAR
replace positions absent from VCF with CHAR

-c, --chain FILE
write a chain file for liftover

-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

-f, --fasta-ref FILE
reference sequence in fasta format

-H, --haplotype 1|2|R|A|I|LR|LA|SR|SA|1pIu|2pIu
choose which allele from the FORMAT/GT field to use (the codes are case-insensitive):

1
the first allele, regardless of phasing

2
the second allele, regardless of phasing

R
the REF allele (in heterozygous genotypes)

A
the ALT allele (in heterozygous genotypes)

I
IUPAC code for all genotypes

LR, LA
the longer allele. If both have the same length, use the REF allele (LR), or the
ALT allele (LA)

SR, SA
the shorter allele. If both have the same length, use the REF allele (SR), or the
ALT allele (SA)

1pIu, 2pIu
first/second allele for phased genotypes and IUPAC code for unphased genotypes

This option requires *-s*, unless exactly one sample is present in the VCF

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.

-I, --iupac-codes
output variants in the form of IUPAC ambiguity codes determined from FORMAT/GT fields.
By default all samples are used and can be subset with -s, --samples and -S,
--samples-file. Use -s - to ignore samples and use only the REF and ALT columns. NOTE:
prior to version 1.17 the IUPAC codes were determined solely from REF,ALT columns and
sample genotypes were not considered.

--mark-del CHAR
instead of removing sequence, insert CHAR for deletions

--mark-ins uc|lc
highlight inserted sequence in uppercase (uc) or lowercase (lc), leaving the rest of
the sequence as is

--mark-snv uc|lc
highlight substitutions in uppercase (uc) or lowercase (lc), leaving the rest of the
sequence as is

-m, --mask FILE
BED file or TAB file with regions to be replaced with N (the default) or as specified
by the next --mask-with option. See discussion of --regions-file in Common Options for
file format details.

--mask-with CHAR|lc|uc
replace sequence from --mask with CHAR, skipping overlapping variants, or change to
lowercase (lc) or uppercase (uc)

-M, --missing CHAR
instead of skipping the missing genotypes, output the character CHAR (e.g. "?")

-o, --output FILE
write output to a file

-s, --samples LIST
apply variants of the listed samples. See also the option -I, --iupac-codes

-S, --samples-file FILE
apply variants of the samples listed in the file. See also the option -I,
--iupac-codes

Examples:

# Apply variants present in sample "NA001", output IUPAC codes for hets
bcftools consensus -i -s NA001 -f in.fa in.vcf.gz > out.fa

# Create consensus for one region. The fasta header lines are then expected
# in the form ">chr:from-to". Ignore samples and consider only the REF and ALT columns
samtools faidx ref.fa 8:11870-11890 | bcftools consensus -s - in.vcf.gz -o out.fa

# For more examples see http://samtools.github.io/bcftools/howtos/consensus-sequence.html

bcftools convert [OPTIONS] FILE
VCF input options:
-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file FILE
see Common Options

--regions-overlap 0|1|2
see Common Options

-s, --samples LIST
see Common Options

-S, --samples-file FILE
see Common Options

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see Common Options

--targets-overlap 0|1|2
see Common Options

VCF output options:
--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v[0-9]
see Common Options

--threads INT
see Common Options

GEN/SAMPLE conversion:
-G, --gensample2vcf prefix or gen-file,sample-file
convert IMPUTE2 output to VCF. One of the ID columns ("SNP ID" or "rsID" in
https://www.cog-genomics.org/plink/2.0/formats#gen) must be of the form
"CHROM:POS_REF_ALT" to detect possible strand swaps.
When the --vcf-ids option is given, the other column (autodetected) is used to fill
the ID column of the VCF.
See also -g and --3N6 options.

-g, --gensample prefix or gen-file,sample-file
convert from VCF to gen/sample format used by IMPUTE2 and SHAPEIT. The columns of .gen
file format are ID1,ID2,POS,A,B followed by three genotype probabilities P(AA), P(AB),
P(BB) for each sample. In order to prevent strand swaps, the program uses IDs of the
form "CHROM:POS_REF_ALT". When the --vcf-ids option is given, the second column is set
to match the ID column of the VCF.
See also -G and --3N6 options.
The file .gen and .sample file format are:

.gen (with --3N6 --vcf-ids)
---------------------------
chr1 1:111485207_G_A rsID1 111485207 G A 0 1 0 0 1 0
chr1 1:111494194_C_T rsID2 111494194 C T 0 1 0 0 0 1

.gen (with --vcf-ids)
---------------------------
1:111485207_G_A rsID1 111485207 G A 0 1 0 0 1 0
1:111494194_C_T rsID2 111494194 C T 0 1 0 0 0 1

.gen (the default)
------------------------------
1:111485207_G_A 1:111485207_G_A 111485207 G A 0 1 0 0 1 0
1:111494194_C_T 1:111494194_C_T 111494194 C T 0 1 0 0 0 1

.sample
-------
ID_1 ID_2 missing
0 0 0
sample1 sample1 0
sample2 sample2 0

--3N6
Expect/Create files in the 3*N+6 column format. This is the new .gen file format with
the first column containing the chromosome name, see
https://www.cog-genomics.org/plink/2.0/formats#gen

--tag STRING
tag to take values for .gen file: GT,PL,GL,GP

--sex FILE
output sex column in the sample file. The FILE format is

MaleSample M
FemaleSample F

--vcf-ids
output VCF IDs in the second column instead of CHROM:POS_REF_ALT

gVCF conversion:
--gvcf2vcf
convert gVCF to VCF, expanding REF blocks into sites. Note that the -i and -e options
work differently with this switch. In this situation the filtering expressions define
which sites should be expanded and which sites should be left unmodified, but all
sites are printed on output. In order to drop sites, stream first through bcftools
view.

-f, --fasta-ref file
reference sequence in fasta format. Must be indexed with samtools faidx

HAP/SAMPLE conversion:
--hapsample2vcf prefix or hap-file,sample-file
convert from hap/sample format to VCF. The columns of .hap file are similar to .gen
file above, but there are only two haplotype columns per sample. Note that the first
or the second column of the .hap file is expected to be in the form
"CHR:POS_REF_ALT[_END]", with the _END being optional for defining the INFO/END tag
when ALT is a symbolic allele. For example:

.hap (with --vcf-ids)
---------------------
1:111485207_G_A rsID1 111485207 G A 0 1 0 0
1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0

.hap (the default)
------------------
1 1:111485207_G_A 111485207 G A 0 1 0 0
1 1:111495231_A_<DEL>_111495784 111495231 A <DEL> 0 0 1 0

--hapsample prefix or hap-file,sample-file
convert from VCF to hap/sample format used by IMPUTE2 and SHAPEIT. The columns of .hap
file begin with ID,RSID,POS,REF,ALT. In order to prevent strand swaps, the program
uses IDs of the form "CHROM:POS_REF_ALT".

--haploid2diploid
with -h option converts haploid genotypes to homozygous diploid genotypes. For
example, the program will print 0 0 instead of the default 0 -. This is useful for
programs which do not handle haploid genotypes correctly.

--sex FILE
output sex column in the sample file. The FILE format is

MaleSample M
FemaleSample F

--vcf-ids
the second column of the .hap file holds the VCF ids, the first column is of the form
"CHR:POS_REF_ALT[_END]". Without the option, the format follows
https://www.cog-genomics.org/plink/2.0/formats#haps with ids (the second column) of
the form "CHR:POS_REF_ALT[_END]"

HAP/LEGEND/SAMPLE conversion:
-H, --haplegendsample2vcf prefix or hap-file,legend-file,sample-file
convert from hap/legend/sample format used by IMPUTE2 to VCF. See also -h,
--hapslegendsample below.

-h, --haplegendsample prefix or hap-file,legend-file,sample-file
convert from VCF to hap/legend/sample format used by IMPUTE2 and SHAPEIT. The columns
of .legend file ID,POS,REF,ALT. In order to prevent strand swaps, the program uses IDs
of the form "CHROM:POS_REF_ALT". The .sample file is quite basic at the moment with
columns for population, group and sex expected to be edited by the user. For example:

.hap
-----
0 1 0 0 1 0
0 1 0 0 0 1

.legend
-------
id position a0 a1
1:111485207_G_A 111485207 G A
1:111494194_C_T 111494194 C T

.sample
-------
sample population group sex
sample1 sample1 sample1 2
sample2 sample2 sample2 2

--sex FILE
output sex column in the sample file. The FILE format is

MaleSample M
FemaleSample F

--vcf-ids
output VCF IDs instead of "CHROM:POS_REF_ALT". Note that this option can be used with
--haplegendsample but not with --haplegendsample2vcf.

TSV conversion:
--tsv2vcf file
convert from TSV (tab-separated values) format (such as generated by 23andMe) to VCF.
The input file fields can be tab- or space- delimited

-c, --columns list
comma-separated list of fields in the input file. In the current version, the fields
CHROM, POS, ID, and AA are expected and can appear in arbitrary order, columns which
should be ignored in the input file can be indicated by "-". The AA field lists
alleles on the forward reference strand, for example "CC" or "CT" for diploid
genotypes or "C" for haploid genotypes (sex chromosomes). Insertions and deletions are
not supported yet, missing data can be indicated with "--".

-f, --fasta-ref file
reference sequence in fasta format. Must be indexed with samtools faidx

-s, --samples LIST
list of sample names. See Common Options

-S, --samples-file FILE
file of sample names. See Common Options

Example:

# Convert 23andme results into VCF
bcftools convert -c ID,CHROM,POS,AA -s SampleName -f 23andme-ref.fa --tsv2vcf 23andme.txt -Oz -o out.vcf.gz

bcftools csq [OPTIONS] FILE
Haplotype aware consequence predictor which correctly handles combined variants such as
MNPs split over multiple VCF records, SNPs separated by an intron (but adjacent in the
spliced transcript) or nearby frame-shifting indels which in combination in fact are not
frame-shifting.

The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the -c
option). The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes. See
the usage examples below for using the %TBCSQ converter in query for extracting a more
human readable form from this bitmask. The construction of the bitmask limits the number
of consequences that can be referenced per sample in the FORMAT/BCSQ tags. By default this
is 15, but if more are required, see the --ncsq option.

The program requires on input a VCF/BCF file, the reference genome in fasta format
(--fasta-ref) and genomic features in the GFF3 format downloadable from the Ensembl
website (--gff-annot), and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3
files are supported.

By default, the input VCF should be phased. If phase is unknown, or only partially known,
the --phase option can be used to indicate how to handle unphased data. Alternatively,
haplotype aware calling can be turned off with the --local-csq option.

If conflicting (overlapping) variants within one haplotype are detected, a warning will be
emitted and predictions will be based on only the first variant in the analysis.

Symbolic alleles are not supported. They will remain unannotated in the output VCF and are
ignored for the prediction analysis.

-c, --custom-tag STRING
use this custom tag to store consequences rather than the default BCSQ tag

-B, --trim-protein-seq INT
abbreviate protein-changing predictions to maximum of INT aminoacids. For example,
instead of writing the whole modified protein sequence with potentially hundreds of
aminoacids, with -B 1 only an abbreviated version such as 25E..329>25G..94 will be
written.

-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

-f, --fasta-ref FILE
reference sequence in fasta format (required)

--force
run even if some sanity checks fail. Currently the option allows to skip transcripts
in malformatted GFFs with incorrect phase

-g, --gff-annot FILE
GFF3 annotation file (required), such as
ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens. An example of a minimal working
GFF file:

# The program looks for "CDS", "exon", "three_prime_UTR" and "five_prime_UTR" lines,
# looks up their parent transcript (determined from the "Parent=transcript:" attribute),
# the gene (determined from the transcript's "Parent=gene:" attribute), and the biotype
# (the most interesting is "protein_coding").
#
# Attributes required for
# gene lines:
# - ID=gene:<gene_id>
# - biotype=<biotype>
# - Name=<gene_name> [optional]
#
# transcript lines:
# - ID=transcript:<transcript_id>
# - Parent=gene:<gene_id>
# - biotype=<biotype>
#
# other lines (CDS, exon, five_prime_UTR, three_prime_UTR):
# - Parent=transcript:<transcript_id>
#
# Supported biotypes:
# - see the function gff_parse_biotype() in bcftools/csq.c

1 ignored_field gene 21 2148 . - . ID=gene:GeneId;biotype=protein_coding;Name=GeneName
1 ignored_field transcript 21 2148 . - . ID=transcript:TranscriptId;Parent=gene:GeneId;biotype=protein_coding
1 ignored_field three_prime_UTR 21 2054 . - . Parent=transcript:TranscriptId
1 ignored_field exon 21 2148 . - . Parent=transcript:TranscriptId
1 ignored_field CDS 21 2148 . - 1 Parent=transcript:TranscriptId
1 ignored_field five_prime_UTR 210 2148 . - . Parent=transcript:TranscriptId

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.

-l, --local-csq
switch off haplotype-aware calling, run localized predictions considering only one VCF
record at a time

-n, --ncsq INT
maximum number of per-haplotype consequences to consider for each site. The INFO/BCSQ
column includes all consequences, but only the first INT will be referenced by the
FORMAT/BCSQ fields. The default value is 15 which corresponds to one 32-bit integer
per diploid sample, after accounting for values reserved by the BCF specification.
Note that increasing the value leads to increased size of the output BCF.

--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type t|b|u|z|v[0-9]
see Common Options. In addition, a custom tab-delimited plain text output can be
printed (t).

-p, --phase a|m|r|R|s
how to handle unphased heterozygous genotypes:

a
take GTs as is, create haplotypes regardless of phase (0/1 → 0|1)

m
merge all GTs into a single haplotype (0/1 → 1, 1/2 → 1)

r
require phased GTs, throw an error on unphased heterozygous GTs

R
create non-reference haplotypes if possible (0/1 → 1|1, 1/2 → 1|2)

s
skip unphased heterozygous GTs

-q, --quiet
suppress warning messages

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file FILE
see Common Options

--regions-overlap 0|1|2
see Common Options

-s, --samples LIST
samples to include or "-" to apply all variants and ignore samples

-S, --samples-file FILE
see Common Options

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see Common Options

--targets-overlap 0|1|2
see Common Options

Examples:

# Basic usage
bcftools csq -f hs37d5.fa -g Homo_sapiens.GRCh37.82.gff3.gz in.vcf -Ob -o out.bcf

# Extract the translated haplotype consequences. The following TBCSQ variations
# are recognised:
# %TBCSQ .. print consequences in all haplotypes in separate columns
# %TBCSQ{0} .. print the first haplotype only
# %TBCSQ{1} .. print the second haplotype only
# %TBCSQ{*} .. print a list of unique consequences present in either haplotype
bcftools query -f'[%CHROM\t%POS\t%SAMPLE\t%TBCSQ\n]' out.bcf

Examples of BCSQ annotation:

# Two separate VCF records at positions 2:122106101 and 2:122106102
# change the same codon. This UV-induced C>T dinucleotide mutation
# has been annotated fully at the position 2:122106101 with
# - consequence type
# - gene name
# - ensembl transcript ID
# - coding strand (+ fwd, - rev)
# - amino acid position (in the coding strand orientation)
# - list of corresponding VCF variants
# The annotation at the second position gives the position of the full
# annotation
BCSQ=missense|CLASP1|ENST00000545861|-|1174P>1174L|122106101G>A+122106102G>A
BCSQ=@122106101

# Stop gained variant
BCSQ=stop_gained|C2orf83|ENST00000264387|-|141W>141*|228476140C>T

# The consequence type of a variant downstream from a stop are prefixed with *
BCSQ=*missense|PER3|ENST00000361923|+|1028M>1028T|7890117T>C

Supported consequence types

3_prime_utr
5_prime_utr
coding_sequence
feature_elongation
frameshift
inframe_altering
inframe_deletion
inframe_insertion
intergenic
intron
missense
non_coding
splice_acceptor
splice_donor
splice_region
start_lost
start_retained
stop_gained
stop_lost
stop_retained
synonymous

See also https://ensembl.org/info/genome/variation/prediction/predicted_data.html

bcftools filter [OPTIONS] FILE
Apply fixed-threshold filters.

-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

-g, --SnpGap INT[:'indel',mnp,bnd,other,overlap]
filter SNPs within INT base pairs of an indel or other other variant type. The
following example demonstrates the logic of --SnpGap 3 applied on a deletion and an
insertion:

The SNPs at positions 1 and 7 are filtered, positions 0 and 8 are not:
0123456789
ref .G.GT..G..
del .A.G-..A..
Here the positions 1 and 6 are filtered, 0 and 7 are not:
0123-456789
ref .G.G-..G..
ins .A.GT..A..

-G, --IndelGap INT
filter clusters of indels separated by INT or fewer base pairs allowing only one to
pass. The following example demonstrates the logic of --IndelGap 2 applied on a
deletion and an insertion:

The second indel is filtered:
012345678901
ref .GT.GT..GT..
del .G-.G-..G-..
And similarly here, the second is filtered:
01 23 456 78
ref .A-.A-..A-..
ins .AT.AT..AT..

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.

--mask [^]REGION
Soft filter regions, prepepend "^" to negate. Requires -s, --soft-filter.

-M, --mask-file [^]FILE
Soft filter regions listed in a file, "^" to negate. Requires -s, --soft-filter.

--mask-overlap 0|1|2
Same as --regions-overlap but for --mask/--mask-file. See Common Options. [1]

-m, --mode [+x]
define behaviour at sites with existing FILTER annotations. The default mode replaces
existing filters of failed sites with a new FILTER string while leaving sites which
pass untouched when non-empty and setting to "PASS" when the FILTER string is absent.
The "+" mode appends new FILTER strings of failed sites instead of replacing them. The
"x" mode resets filters of sites which pass to "PASS". Modes "+" and "x" can both be
set.

--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v[0-9]
see Common Options

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

-s, --soft-filter STRING|+
annotate FILTER column with STRING or, with +, a unique filter name generated by the
program ("Filter%d").

-S, --set-GTs .|0
set genotypes of failed samples to missing value (.) or reference allele (0)

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

--targets-overlap 0|1|2
see Common Options

--threads INT
see Common Options

bcftools gtcheck [OPTIONS] [-g genotypes.vcf.gz] query.vcf.gz
Checks sample identity. The program can operate in two modes. If the -g option is given,
the identity of samples from query.vcf.gz is checked against the samples in the -g file.
Without the -g option, multi-sample cross-check of samples in query.vcf.gz is performed.

--distinctive-sites NUM[,MEM[,DIR]]
Find sites that can distinguish between at least NUM sample pairs. If the number is
smaller or equal to 1, it is interpreted as the fraction of pairs. The optional MEM
string sets the maximum memory used for in-memory sorting and DIR is the temporary
directory for external sorting. This option requires also --pairs to be given.

--dry-run
Stop after first record to estimate required time.

-e, --error-probability INT
Interpret genotypes and genotype likelihoods probabilistically. The value of INT
represents genotype quality when GT tag is used (e.g. Q=30 represents one error in
1,000 genotypes and Q=40 one error in 10,000 genotypes) and is ignored when PL tag is
used (in that case an arbitrary non-zero integer can be provided). See also the -u,
--use option below. If set to 0, the discordance equals to the number of mismatching
genotypes when GT vs GT is compared. Note that the values with and without -e are not
comparable, only values generated with -e 0 correspond to mismatching genotypes. If
performance is an issue, set to 0 for faster run but less accurate results.

-g, --genotypes FILE
VCF/BCF file with reference genotypes to compare against

-H, --homs-only
Homozygous genotypes only, useful with low coverage data (requires -g, --genotypes)

--n-matches INT
Print only top INT matches for each sample, 0 for unlimited. Use negative value to
sort by HWE probability rather than the number of discordant sites. Note that average
score is used to determine the top matches, not absolute values.

--no-HWE-prob
Disable calculation of HWE probability to reduce memory requirements with comparisons
between very large number of sample pairs.

-p, --pairs LIST
A comma-separated list of sample pairs to compare. When the -g option is given, the
first sample must be from the query file, the second from the -g file, third from the
query file etc (qry,gt[,qry,gt..]). Without the -g option, the pairs are created the
same way but both samples are from the query file (qry,qry[,qry,qry..])

-P, --pairs-file FILE
A file with tab-delimited sample pairs to compare. The first sample in the pair must
come from the query file, the second from the genotypes file when -g is given

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
Restrict to comma-separated list of regions, see Common Options

*-R, --regions-file' FILE
Restrict to regions listed in a file, see Common Options

--regions-overlap 0|1|2
see Common Options

-s, --samples [qry|gt]:'LIST': List of query samples or -g samples. If neither -s nor -S
are given, all possible sample pair combinations are compared

-S, --samples-file [qry|gt]:'FILE' File with the query or -g samples to compare. If
neither -s nor -S are given, all possible sample pair combinations are compared

-t, --targets file
see Common Options

-T, --targets-file file
see Common Options

--targets-overlap 0|1|2
see Common Options

-u, --use TAG1[,TAG2]
specifies which tag to use in the query file (TAG1) and the -g (TAG2) file. By
default, the PL tag is used in the query file and GT in the -g file when available.

Examples:

# Check discordance of all samples from B against all sample in A
bcftools gtcheck -g A.bcf B.bcf

# Limit comparisons to the fiven list of samples
bcftools gtcheck -s gt:a1,a2,a3 -s qry:b1,b2 -g A.bcf B.bcf

# Compare only two pairs a1,b1 and a1,b2
bcftools gtcheck -p a1,b1,a1,b2 -g A.bcf B.bcf

bcftools head [OPTIONS] [FILE]
By default, prints all headers from the specified input file to standard output in VCF
format. The input file may be in VCF or BCF format; if no FILE is specified, standard
input will be read. With appropriate options, only some of the headers and/or additionally
some of the variant records will be printed.

The bcftools head command outputs VCF headers almost exactly as they appear in the input
file: it may add a ##FILTER=<ID=PASS> header if not already present, but it never adds
version or command line information itself.

Options:
-h, --header INT
Display only the first INT header lines. By default, all header lines are displayed.

-n, --records INT
Also display the first INT variant records. By default, no variant records are
displayed.

bcftools index [OPTIONS] in.bcf|in.vcf.gz
Creates index for bgzip compressed VCF/BCF files for random access. CSI (coordinate-sorted
index) is created by default. The CSI format supports indexing of chromosomes up to length
2^31. TBI (tabix index) index files, which support chromosome lengths up to 2^29, can be
created by using the -t/--tbi option or using the tabix program packaged with htslib. When
loading an index file, bcftools will try the CSI first and then the TBI.

Indexing options:
-c, --csi
generate CSI-format index for VCF/BCF files [default]

-f, --force
overwrite index if it already exists

-m, --min-shift INT
set minimal interval size for CSI indices to 2^INT; default: 14

-o, --output FILE
output file name. If not set, then the index will be created using the input file name
plus a .csi or .tbi extension

-t, --tbi
generate TBI-format index for VCF files

--threads INT
see Common Options

Stats options:
-a, --all
Used in conjunction with -s, --stats, print per contig stats for all contigs, even
those with zero records and those for which no stats are recorded in the index file
(shown as .).

-n, --nrecords
print the number of records based on the CSI or TBI index files

-s, --stats
Print per contig stats based on the CSI or TBI index files. Output format is three
tab-delimited columns listing the contig name, contig length (. if unknown) and number
of records for the contig. Contigs with zero records are not printed by default.

bcftools isec [OPTIONS] A.vcf.gz B.vcf.gz [...]
Creates intersections, unions and complements of VCF files. Depending on the options, the
program can output records from one (or more) files which have (or do not have)
corresponding records with the same position in the other files.

-C, --complement
output positions present only in the first file but missing in the others

-e, --exclude -|EXPRESSION
exclude sites for which EXPRESSION is true. If -e (or -i) appears only once, the same
filtering expression will be applied to all input files. Otherwise, -e or -i must be
given for each input file. To indicate that no filtering should be performed on a
file, use "-" in place of EXPRESSION, as shown in the example below. For valid
expressions see EXPRESSIONS.

-f, --apply-filters LIST
see Common Options

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. See discussion of -e, --exclude
above.

-n, --nfiles [+-=]INT|~BITMAP
output positions present in this many (=), this many or more (+), this many or fewer
(-), or the exact same (~) files

-o, --output FILE
see Common Options. When several files are being output, their names are controlled
via -p instead.

-O, --output-type b|u|z|v[0-9]
see Common Options

-p, --prefix DIR
if given, subset each of the input files accordingly. See also -w.

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

--targets-overlap 0|1|2
see Common Options

-w, --write LIST
list of input files to output given as 1-based indices. With -p and no -w, all files
are written.

Examples:
Create intersection and complements of two sets saving the output in dir/*

bcftools isec -p dir A.vcf.gz B.vcf.gz

Filter sites in A (require INFO/MAF>=0.01) and B (require INFO/dbSNP) but not in C, and
create an intersection, including only sites which appear in at least two of the files
after filters have been applied

bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e- A.vcf.gz B.vcf.gz C.vcf.gz -n +2 -p dir

Extract and write records from A shared by both A and B using exact allele match

bcftools isec -p dir -n=2 -w1 A.vcf.gz B.vcf.gz

Extract records private to A or B comparing by position only

bcftools isec -p dir -n-1 -c all A.vcf.gz B.vcf.gz

Print a list of records which are present in A and B but not in C and D

bcftools isec -n~1100 -c all A.vcf.gz B.vcf.gz C.vcf.gz D.vcf.gz

bcftools merge [OPTIONS] A.vcf.gz B.vcf.gz [...]
Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample
file. For example, when merging file A.vcf.gz containing samples S1, S2 and S3 and file
B.vcf.gz containing samples S3 and S4, the output file will contain five samples named S1,
S2, S3, 2:S3 and S4.

Note that it is responsibility of the user to ensure that the sample names are unique
across all files. If they are not, the program will exit with an error unless the option
--force-samples is given. The sample names can be also given explicitly using the
--print-header and --use-header options.

Note that only records from different files can be merged, never from the same file. For
"vertical" merge take a look at bcftools concat or bcftools norm -m instead.

--force-samples
if the merged files contain duplicate samples names, proceed anyway. Duplicate sample
names will be resolved by prepending the index of the file as it appeared on the
command line to the conflicting sample name (see 2:S3 in the above example).

--print-header
print only merged header and exit

--use-header FILE
use the VCF header in the provided text FILE

-0 --missing-to-ref
assume genotypes at missing sites are 0/0

-f, --apply-filters LIST
see Common Options

-F, --filter-logic x|+
Set the output record to PASS if any of the inputs is PASS (x), or apply all filters
(+), which is the default.

-g, --gvcf -|FILE
merge gVCF blocks, INFO/END tag is expected. If the reference fasta file FILE is not
given and the dash (-) is given, unknown reference bases generated at gVCF block
splits will be substituted with N’s. The --gvcf option uses the following default INFO
rules: -i QS:sum,MinDP:min,I16:sum,IDV:max,IMF:max.

-i, --info-rules -|TAG:METHOD[,...]
Rules for merging INFO fields (scalars or vectors) or - to disable the default rules.
METHOD is one of sum, avg, min, max, join. Default is DP:sum,DP4:sum if these fields
exist in the input files. Fields with no specified rule will take the value from the
first input file. The merged QUAL value is currently set to the maximum. This
behaviour is not user controllable at the moment.

-l, --file-list FILE
Read file names from FILE, one file name per line.

-L, --local-alleles INT
Sites with many alternate alleles can require extremely large storage space which can
exceed the 2GB size limit representable by BCF. This is caused by Number=G tags (such
as FORMAT/PL) which store a value for each combination of reference and alternate
alleles. The -L, --local-alleles option allows to replace such tags with a localized
tag (FORMAT/LPL) which only includes a subset of alternate alleles relevant for that
sample. A new FORMAT/LAA tag is added which lists 1-based indices of the alternate
alleles relevant (local) for the current sample. The number INT gives the maximum
number of alternate alleles that can be included in the PL tag. The default value is 0
which disables the feature and outputs values for all alternate alleles.

-m none .. no new multiallelics, output multiple records instead
-m snps .. allow multiallelic SNP records
-m indels .. allow multiallelic indel records
-m both .. both SNP and indel records can be multiallelic
-m all .. SNP records can be merged with indel records
-m snp-ins-del .. allow multiallelic SNVs, insertions, deletions, but don't mix them
-m id .. merge by ID

--no-index
the option allows to merge files without indexing them first. In order for this option
to work, the user must ensure that the input files have chromosomes in the same order
and consistent with the order of sequences in the VCF header.

--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v[0-9]
see Common Options

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

--threads INT
see Common Options

bcftools mpileup [OPTIONS] -f ref.fa in.bam [in2.bam [...]]
Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or
CRAM) files. This is based on the original samtools mpileup command (with the -v or -g
options) producing genotype likelihoods in VCF or BCF format, but not the textual pileup
output. The mpileup command was transferred to bcftools in order to avoid errors resulting
from use of incompatible versions of samtools and bcftools when using in the
mpileup+bcftools call pipeline.

Individuals are identified from the SM tags in the @RG header lines. Multiple individuals
can be pooled in one alignment file, also one individual can be separated into multiple
files. If sample identifiers are absent, each input file is regarded as one sample.

Note that there are two orthogonal ways to specify locations in the input file; via -r
region and -t positions. The former uses (and requires) an index to do random access while
the latter streams through the file contents filtering out the specified regions,
requiring no index. The two may be used in conjunction. For example a BED file containing
locations of genes in chromosome 20 could be specified using -r 20 -t chr20.bed, meaning
that the index is used to find chromosome 20 and then it is filtered for the regions
listed in the BED file. Also note that the -r option can be much slower than -t with many
regions and can require more memory when multiple regions and many alignment files are
processed.

Input options
-6, --illumina1.3+
Assume the quality is in the Illumina 1.3+ encoding.

-A, --count-orphans
Do not skip anomalous read pairs in variant calling.

-b, --bam-list FILE
List of input alignment files, one file per line [null]

-B, --no-BAQ
Disable probabilistic realignment for the computation of base alignment quality (BAQ).
BAQ is the Phred-scaled probability of a read base being misaligned. Applying this
option greatly helps to reduce false SNPs caused by misalignments.

-C, --adjust-MQ INT
Coefficient for downgrading mapping quality for reads containing excessive
mismatches. Given a read with a phred-scaled probability q of being generated from the
mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value
(the default) disables this functionality.

-D, --full-BAQ
Run the BAQ algorithm on all reads, not just those in problematic regions. This
matches the behaviour for Bcftools 1.12 and earlier.

By default mpileup uses heuristics to decide when to apply the BAQ algorithm. Most
sequences will not be BAQ adjusted, giving a CPU time closer to --no-BAQ, but it will
still be applied in regions with suspected problematic alignments. This has been
tested to work well on single sample data with even allele frequency, but the
reliability is unknown for multi-sample calling and for low allele frequency variants
so full BAQ is still recommended in those scenarios.

-d, --max-depth INT
At a position, read maximally INT reads per input file. Note that the original
samtools mpileup command had a minimum value of 8000/n where n was the number of input
files given to mpileup. This means that in samtools mpileup the default was highly
likely to be increased and the -d parameter would have an effect only once above the
cross-sample minimum of 8000. This behavior was problematic when working with a
combination of single- and multi-sample bams, therefore in bcftools mpileup the user
is given the full control (and responsibility), and an informative message is printed
instead [250]

-E, --redo-BAQ
Recalculate BAQ on the fly, ignore existing BQ tags

-f, --fasta-ref FILE
The faidx-indexed reference file in the FASTA format. The file can be optionally
compressed by bgzip. Reference is required by default unless the --no-reference option
is set [null]

--no-reference
Do not require the --fasta-ref option.

-G, --read-groups FILE
list of read groups to include or exclude if prefixed with "^". One read group per
line. This file can also be used to assign new sample names to read groups by giving
the new sample name as a second white-space-separated field, like this: "read_group_id
new_sample_name". If the read group name is not unique, also the bam file name can be
included: "read_group_id file_name sample_name". If all reads from the alignment file
should be treated as a single sample, the asterisk symbol can be used: "* file_name
sample_name". Alignments without a read group ID can be matched with "?". NOTE: The
meaning of bcftools mpileup -G is the opposite of samtools mpileup -G.

RG_ID_1
RG_ID_2 SAMPLE_A
RG_ID_3 SAMPLE_A
RG_ID_4 SAMPLE_B
RG_ID_5 FILE_1.bam SAMPLE_A
RG_ID_6 FILE_2.bam SAMPLE_A
* FILE_3.bam SAMPLE_C
? FILE_3.bam SAMPLE_D

--indels-2.0
A new EXPERIMENTAL indel calling model which aims to address some known deficiencies
of the current indel calling algorithm. Specifically, it uses diploid reference
consensus sequence. Note that in the current version it has the potential to increase
sensitivity but at the cost of decreased specificity

-q, -min-MQ INT
Minimum mapping quality for an alignment to be used [0]

-Q, --min-BQ INT
Minimum base quality for a base to be considered [13]

--max-BQ INT
Caps the base quality to a maximum value [60]. This can be particularly useful on
technologies that produce overly optimistic high qualities, leading to too many false
positives or incorrect genotype assignments.

-r, --regions CHR|CHR:POS|CHR:FROM-TO|CHR:FROM-[,...]
Only generate mpileup output in given regions. Requires the alignment files to be
indexed. If used in conjunction with -l then considers the intersection; see Common
Options

-R, --regions-file FILE
As for -r, --regions, but regions read from FILE; see Common Options

--regions-overlap 0|1|2
see Common Options

--ignore-RG
Ignore RG tags. Treat all reads in one alignment file as one sample.

--ls, --skip-all-set
Skip reads with all of the FLAG bits set [null]

--ns, --skip-any-set
Skip reads with any of the FLAG bits set. This option replaces and is synonymous to
the deprecated --ff, --excl-flags [UNMAP,SECONDARY,QCFAIL,DUP]

--lu, --skip-all-unset
Skip reads with all of the FLAG bits unset. This option replaces and is synonymous to
the deprecated --rf, --incl-flags [null]

--nu, --skip-any-unset
Skip reads with any of the FLAG bits unset [null]

-s, --samples LIST
list of sample names. See Common Options

-S, --samples-file FILE
file of sample names to include or exclude if prefixed with "^". One sample per line.
This file can also be used to rename samples by giving the new sample name as a second
white-space-separated column, like this: "old_name new_name". If a sample name
contains spaces, the spaces can be escaped using the backslash character, for example
"Not\ a\ good\ sample\ name".

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see Common Options

--targets-overlap 0|1|2
see Common Options

-x, --ignore-overlaps
Disable read-pair overlap detection.

--seed INT
Set the random number seed used when sub-sampling deep regions [0].

Output options
-a, --annotate LIST
Comma-separated list of FORMAT and INFO tags to output. (case-insensitive, the
"FORMAT/" prefix is optional, and use "?" to list available annotations on the command
line) [null]:

FORMAT/AD .. Allelic depth (Number=R,Type=Integer)
FORMAT/ADF .. Allelic depths on the forward strand (Number=R,Type=Integer)
FORMAT/ADR .. Allelic depths on the reverse strand (Number=R,Type=Integer)
FORMAT/DP .. Number of high-quality bases (Number=1,Type=Integer)
FORMAT/SP .. Phred-scaled strand bias P-value (Number=1,Type=Integer)
FORMAT/SCR .. Number of soft-clipped reads (Number=1,Type=Integer)

INFO/AD .. Total allelic depth (Number=R,Type=Integer)
INFO/ADF .. Total allelic depths on the forward strand (Number=R,Type=Integer)
INFO/ADR .. Total allelic depths on the reverse strand (Number=R,Type=Integer)
INFO/SCR .. Number of soft-clipped reads (Number=1,Type=Integer)

FORMAT/DV .. Deprecated in favor of FORMAT/AD; Number of high-quality non-reference bases, (Number=1,Type=Integer)
FORMAT/DP4 .. Deprecated in favor of FORMAT/ADF and FORMAT/ADR; Number of high-quality ref-forward, ref-reverse,
alt-forward and alt-reverse bases (Number=4,Type=Integer)
FORMAT/DPR .. Deprecated in favor of FORMAT/AD; Number of high-quality bases for each observed allele (Number=R,Type=Integer)
INFO/DPR .. Deprecated in favor of INFO/AD; Number of high-quality bases for each observed allele (Number=R,Type=Integer)

-g, --gvcf INT[,...]
output gVCF blocks of homozygous REF calls, with depth (DP) ranges specified by the
list of integers. For example, passing 5,15 will group sites into two types of gVCF
blocks, the first with minimum per-sample DP from the interval [5,15) and the latter
with minimum depth 15 or more. In this example, sites with minimum per-sample depth
less than 5 will be printed as separate records, outside of gVCF blocks.

--no-version
see Common Options

-o, --output FILE
Write output to FILE, rather than the default of standard output. (The same short
option is used for both --open-prob and --output. If -o's argument contains any
non-digit characters other than a leading + or - sign, it is interpreted as
--output. Usually the filename extension will take care of this, but to write to an
entirely numeric filename use -o ./123 or --output 123.)

-O, --output-type b|u|z|v[0-9]
see Common Options

--threads INT
see Common Options

-U, --mwu-u
The the previous Mann-Whitney U test score from version 1.12 and earlier. This is a
probability score, but importantly it folds probabilities above or below the desired
score into the same P. The new Mann-Whitney U test score is a "Z score", expressing
the score as the number of standard deviations away from the mean (with zero being
matching the mean). It keeps both positive and negative values. This can be important
for some tests where errors are asymmetric.

This option changes the INFO field names produced back to the ones
used by the earlier Bcftools releases. For excample BQBZ becomes
BQB.

Options for SNP/INDEL genotype likelihood computation
-X, --config STR
Specify a platform specific configuration profile. The profile should be one of 1.12,
illumina, ont or pacbio-ccs. Settings applied are as follows:

1.12 -Q13 -h100 -m1
illumina [ default values ]
ont -B -Q5 --max-BQ 30 -I
pacbio-ccs -D -Q5 --max-BQ 50 -F0.1 -o25 -e1 -M99999

--ar, --ambig-reads drop|incAD|incAD0
What to do with ambiguous indel reads that do not span an entire short tandem repeat
region: discard ambiguous reads from calling and do not increment high-quality AD
depth counters (drop), exclude from calling but increment AD counters proportionally
(incAD), exclude from calling and increment the first value of the AD counter (incAD0)
[drop]

-e, --ext-prob INT
Phred-scaled gap extension sequencing error probability. Reducing INT leads to longer
indels [20]

-F, --gap-frac FLOAT
Minimum fraction of gapped reads [0.002]

-h, --tandem-qual INT
Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the
sequencing error of an indel of size s is modeled as INT*s/l [500] Increasing this
informs the caller that indels in long homopolymers are more likely genuine and less
likely to be sequencing artifacts. Hence increasing tandem-qual will have higher
recall and lower precision. Bcftools 1.12 and earlier had a default of 100, which was
tuned around more error prone instruments. Note changing this may have a minor impact
on SNP calling too. For maximum SNP calling accuracy, it may be preferable to adjust
this lower again, although this will adversely affect indels.

--indel-bias FLOAT
Skews the indel scores up or down, trading recall (low false-negative) vs precision
(low false-positive) [1.0]. In Bcftools 1.12 and earlier this parameter didn’t exist,
but had an implied value of 1.0. If you are planning to do heavy filtering of
variants, selecting the best quality ones only (favouring precision over recall), it
is advisable to set this lower (such as 0.75) while higher depth samples or where you
favour recall rates over precision may work better with a higher value such as 2.0.

--indel-size INT
Indel window size to use when assessing the quality of candidate indels. Note that
although the window size approximately corresponds to the maximum indel size
considered, it is not an exact threshold [110]

-I, --skip-indels
Do not perform INDEL calling

-L, --max-idepth INT
Skip INDEL calling if the average per-sample depth is above INT [250]

-m, --min-ireads INT
Minimum number gapped reads for indel candidates INT [1]

-M, --max-read-len INT
The maximum read length permitted by the BAQ algorithm [500]. Variants are still
called on longer reads, but they will not be passed through the BAQ method. This limit
exists to prevent excessively long BAQ times and high memory usage. Note if partial
BAQ is enabled with -D then raising this parameter will likely not have a significant
a CPU cost.

-o, --open-prob INT
Phred-scaled gap open sequencing error probability. Reducing INT leads to more indel
calls. (The same short option is used for both --open-prob and --output. When -o’s
argument contains only an optional + or - sign followed by the digits 0 to 9, it is
interpreted as --open-prob.) [40]

-p, --per-sample-mF
Apply -m and -F thresholds per sample to increase sensitivity of calling. By default
both options are applied to reads pooled from all samples.

-P, --platforms STR
Comma-delimited list of platforms (determined by @RG-PL) from which indel
candidates are obtained. It is recommended to collect indel candidates from sequencing
technologies that have low indel error rate such as ILLUMINA [all]

Examples:
Call SNPs and short INDELs, then mark low quality sites and sites with the read depth
exceeding a limit. (The read depth should be adjusted to about twice the average read
depth as higher read depths usually indicate problematic regions which are often enriched
for artefacts.) One may consider to add -C50 to mpileup if mapping quality is
overestimated for reads containing excessive mismatches. Applying this option usually
helps for BWA-backtrack alignments, but may not other aligners.

bcftools mpileup -Ou -f ref.fa aln.bam | \
bcftools call -Ou -mv | \
bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > var.flt.vcf

bcftools norm [OPTIONS] file.vcf.gz
Left-align and normalize indels, check if REF alleles match the reference, split
multiallelic sites into multiple rows; recover multiallelics from multiple rows.
Left-alignment and normalization will only be applied if the --fasta-ref option is
supplied.

-a, --atomize
Decompose complex variants, e.g. split MNVs into consecutive SNVs. See also
--atom-overlaps and --old-rec-tag.

--atom-overlaps .|*
Alleles missing because of an overlapping variant can be set either to missing (.) or
to the star alele (*), as recommended by the VCF specification. IMPORTANT: Note that
asterisk is expaneded by shell and must be put in quotes or escaped by a backslash:

# Before atomization:
100 CC C,GG 1/2

# After:
# bcftools norm -a .
100 C G ./1
100 CC C 1/.
101 C G ./1

# After:
# bcftools norm -a '*'
# bcftools norm -a \*
100 C G,* 2/1
100 CC C,* 1/2
101 C G,* 2/1

-c, --check-ref e|w|x|s
what to do when incorrect or missing REF allele is encountered: exit (e), warn (w),
exclude (x), or set/fix (s) bad sites. The w option can be combined with x and s. Note
that s can swap alleles and will update genotypes (GT) and AC counts, but will not
attempt to fix PL or other fields. Also note, and this cannot be stressed enough, that
s will NOT fix strand issues in your VCF, do NOT use it for that purpose!!! (Instead
see http://samtools.github.io/bcftools/howtos/plugin.af-dist.html and
http://samtools.github.io/bcftools/howtos/plugin.fixref.html.)

-d, --rm-dup snps|indels|both|all|exact
If a record is present multiple times, output only the first instance. See also
--collapse in Common Options.

-D, --remove-duplicates
If a record is present in multiple files, output only the first instance. Alias for -d
none, deprecated.

-f, --fasta-ref FILE
reference sequence. Supplying this option will turn on left-alignment and
normalization, however, see also the --do-not-normalize option below.

--force
try to proceed with -m- even if malformed tags with incorrect number of fields are
encountered, discarding such tags. (Experimental, use at your own risk.)

--keep-sum TAG[,...]
keep vector sum constant when splitting multiallelic sites. Only AD tag is currently
supported. See also https://github.com/samtools/bcftools/issues/360

-m, --multiallelics -|+[snps|indels|both|any]
split multiallelic sites into biallelic records (-) or join biallelic sites into
multiallelic records (+). An optional type string can follow which controls variant
types which should be split or merged together: If only SNP records should be split or
merged, specify snps; if both SNPs and indels should be merged separately into two
records, specify both; if SNPs and indels should be merged into a single record,
specify any.

--multi-overlaps 0|.
use the reference (0) or missing (.) allele for overlapping alleles after splitting
multiallelic sites

--no-version
see Common Options

-N, --do-not-normalize
the -c s option can be used to fix or set the REF allele from the reference -f. The -N
option will not turn on indel normalisation as the -f option normally implies

--old-rec-tag STR
Add INFO/STR annotation with the original record. The format of the annotation is
CHROM|POS|REF|ALT|USED_ALT_IDX.

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v[0-9]
see Common Options

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

-s, --strict-filter
when merging (-m+), merged site is PASS only if all sites being merged PASS

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see Common Options

--targets-overlap 0|1|2
see Common Options

--threads INT
see Common Options

-w, --site-win INT
maximum distance between two records to consider when locally sorting variants which
changed position during the realignment

bcftools [plugin NAME|+NAME] [OPTIONS] FILE — [PLUGIN OPTIONS]
A common framework for various utilities. The plugins can be used the same way as normal
commands only their name is prefixed with "+". Most plugins accept two types of
parameters: general options shared by all plugins followed by a separator, and a list of
plugin-specific options. There are some exceptions to this rule, some plugins do not
accept the common options and implement their own parameters. Therefore please pay
attention to the usage examples that each plugin comes with.

VCF input options:
-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

--targets-overlap 0|1|2
see Common Options

VCF output options:
--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v[0-9]
see Common Options

--threads INT
see Common Options

Plugin options:
-h, --help
list plugin’s options

-l, --list-plugins
List all available plugins.

By default, appropriate system directories are searched for installed plugins. You can
override this by setting the BCFTOOLS_PLUGINS environment variable to a
colon-separated list of directories to search. If BCFTOOLS_PLUGINS begins with a
colon, ends with a colon, or contains adjacent colons, the system directories are also
searched at that position in the list of directories.

-v, --verbose
print debugging information to debug plugin failure

-V, --version
print version string and exit

List of plugins coming with the distribution:
ad-bias
find positions with wildly varying ALT allele frequency (Fisher test on FMT/AD)

add-variantkey
add VariantKey INFO fields VKX and RSX

af-dist
collect AF deviation stats and GT probability distribution given AF and assuming HWE

allele-length
count the frequency of the length of REF, ALT and REF+ALT

check-ploidy
check if ploidy of samples is consistent for all sites

check-sparsity
print samples without genotypes in a region or chromosome

color-chrs
color shared chromosomal segments, requires trio VCF with phased GTs

contrast
runs a basic association test, per-site or in a region, and checks for novel alleles
and genotypes in two groups of samples. Adds the following INFO annotations:

• PASSOC .. Fisher’s exact test probability of genotypic association (REF vs
non-REF allele)

• FASSOC .. proportion of non-REF allele in controls and cases

• NASSOC .. number of control-ref, control-alt, case-ref and case-alt alleles

• NOVELAL .. lists samples with a novel allele not observed in the control group

• NOVELGT .. lists samples with a novel genotype not observed in the control group

counts
a minimal plugin which counts number of SNPs, Indels, and total number of sites.

dosage
print genotype dosage. By default the plugin searches for PL, GL and GT, in that
order.

fill-from-fasta
fill INFO or REF field based on values in a fasta file

fill-tags
set various INFO tags. The list of tags supported in this version:

• INFO/AC Number:A Type:Integer .. Allele count in genotypes

• INFO/AC_Hom Number:A Type:Integer .. Allele counts in homozygous genotypes

• INFO/AC_Het Number:A Type:Integer .. Allele counts in heterozygous genotypes

• INFO/AC_Hemi Number:A Type:Integer .. Allele counts in hemizygous genotypes

• INFO/AF Number:A Type:Float .. Allele frequency

• INFO/AN Number:1 Type:Integer .. Total number of alleles in called
genotypes

• INFO/ExcHet Number:A Type:Float .. Test excess heterozygosity; 1=good,
0=bad

• INFO/END Number:1 Type:Integer .. End position of the variant

• INFO/F_MISSING Number:1 Type:Float .. Fraction of missing genotypes

• INFO/HWE Number:A Type:Float .. HWE test (PMID:15789306); 1=good, 0=bad

• INFO/MAF Number:A Type:Float .. Minor Allele frequency

• INFO/NS Number:1 Type:Integer .. Number of samples with data

• INFO/TYPE Number:. Type:String .. The record type (REF,SNP,MNP,INDEL,etc)

• FORMAT/VAF Number:A Type:Float .. The fraction of reads with the
alternate allele, requires FORMAT/AD or ADF+ADR

• FORMAT/VAF1 Number:1 Type:Float .. The same as FORMAT/VAF but for all
alternate alleles cumulatively

• TAG=func(TAG) Number:1 Type:Integer .. Experimental support for user-defined
expressions such as "DP=sum(DP)"

fixploidy
sets correct ploidy

fixref
determine and fix strand orientation

frameshifts
annotate frameshift indels

GTisec
count genotype intersections across all possible sample subsets in a vcf file

GTsubset
output only sites where the requested samples all exclusively share a genotype

guess-ploidy
determine sample sex by checking genotype likelihoods (GL,PL) or genotypes (GT) in the
non-PAR region of chrX.

gvcfz
compress gVCF file by resizing non-variant blocks according to specified criteria

impute-info
add imputation information metrics to the INFO field based on selected FORMAT tags

indel-stats
calculates per-sample or de novo indels stats. The usage and format is similar to
smpl-stats and trio-stats

isecGT
compare two files and set non-identical genotypes to missing

mendelian
count Mendelian consistent / inconsistent genotypes (deprecated, use +mendelian2
instead)

mendelian2
count Mendelian consistent / inconsistent genotypes.

missing2ref
sets missing genotypes ("./.") to ref allele ("0/0" or "0|0")

parental-origin
determine parental origin of a CNV region

prune
prune sites by missingness, allele frequency or linkage disequilibrium. Alternatively,
annotate sites with r2, Lewontin’s D' (PMID:19433632), Ragsdale’s D (PMID:31697386).

remove-overlaps
remove overlapping variants and duplicate sites

scatter
intended as an inverse to bcftools concat, scatter VCF by chunks or regions, creating
multiple VCFs.

setGT
general tool to set genotypes according to rules requested by the user

smpl-stats
calculates basic per-sample stats. The usage and format is similar to indel-stats and
trio-stats.

split
split VCF by sample, creating single- or multi-sample VCFs

split-vep
extract fields from structured annotations such as INFO/CSQ created by bcftools/csq or
VEP. These can be added as a new INFO field to the VCF or in a custom text format. See
http://samtools.github.io/bcftools/howtos/plugin.split-vep.html for more.

tag2tag
Convert between similar tags, such as GL,PL,GP or QR,QA,QS.

trio-dnm2
screen variants for possible de-novo mutations in trios

trio-stats
calculate transmission rate in trio children. The usage and format is similar to
indel-stats and smpl-stats.

trio-switch-rate
calculate phase switch rate in trio samples, children samples must have phased GTs

variant-distance
annotate sites with the distance to the nearest variant

variantkey-hex
generate unsorted VariantKey-RSid index files in hexadecimal format

Examples:
# List options common to all plugins
bcftools plugin

# List available plugins
bcftools plugin -l

# Run a plugin
bcftools plugin counts in.vcf

# Run a plugin using the abbreviated "+" notation
bcftools +counts in.vcf

# Run a plugin from an explicit location
bcftools +/path/to/counts.so in.vcf

# The input VCF can be streamed just like in other commands
cat in.vcf | bcftools +counts

# Print usage information of plugin "dosage"
bcftools +dosage -h

# Replace missing genotypes with 0/0
bcftools +missing2ref in.vcf

# Replace missing genotypes with 0|0
bcftools +missing2ref in.vcf -- -p

Plugins troubleshooting:
Things to check if your plugin does not show up in the bcftools plugin -l output:

• Run with the -v option for verbose output: bcftools plugin -lv

• Does the environment variable BCFTOOLS_PLUGINS include the correct path?

Plugins API:
// Short description used by 'bcftools plugin -l'
const char *about(void);

// Longer description used by 'bcftools +name -h'
const char *usage(void);

// Called once at startup, allows initialization of local variables.
// Return 1 to suppress normal VCF/BCF header output, -1 on critical
// errors, 0 otherwise.
int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr);

// Called for each VCF record, return NULL to suppress the output
bcf1_t *process(bcf1_t *rec);

// Called after all lines have been processed to clean up
void destroy(void);

bcftools polysomy [OPTIONS] file.vcf.gz
Detect number of chromosomal copies in VCFs annotates with the Illumina’s B-allele
frequency (BAF) values. Note that this command is not compiled in by default, see the
section Optional Compilation with GSL in the INSTALL file for help.

General options:
-o, --output-dir path
output directory

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

-s, --sample string
sample name

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see Common Options

--targets-overlap 0|1|2
see Common Options

-v, --verbose
verbose debugging output which gives hints about the thresholds and decisions made by
the program. Note that the exact output can change between versions.

Algorithm options:
-b, --peak-size float
the minimum peak size considered as a good match can be from the interval [0,1] where
larger is stricter

-c, --cn-penalty float
a penalty for increasing copy number state. How this works: multiple peaks are always
a better fit than a single peak, therefore the program prefers a single peak (normal
copy number) unless the absolute deviation of the multiple peaks fit is significantly
smaller. Here the meaning of "significant" is given by the float from the interval
[0,1] where larger is stricter.

-f, --fit-th float
threshold for goodness of fit (normalized absolute deviation), smaller is stricter

-i, --include-aa
include also the AA peak in CN2 and CN3 evaluation. This usually requires increasing
-f.

-m, --min-fraction float
minimum distinguishable fraction of aberrant cells. The experience shows that
trustworthy are estimates of 20% and more.

-p, --peak-symmetry float
a heuristics to filter failed fits where the expected peak symmetry is violated. The
float is from the interval [0,1] and larger is stricter

bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz [...]]
Extracts fields from VCF or BCF files and outputs them in user-defined format.

-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

--force-samples
continue even when some samples requested via -s/-S do not exist

-f, --format FORMAT
learn by example, see below

-H, --print-header
print header

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.

-l, --list-samples
list sample names and exit

-o, --output FILE
see Common Options

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

-s, --samples LIST
see Common Options

-S, --samples-file FILE
see Common Options

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

--targets-overlap 0|1|2
see Common Options

-u, --allow-undef-tags
do not throw an error if there are undefined tags in the format string, print "."
instead

-v, --vcf-list FILE
process multiple VCFs listed in the file

Format:
%CHROM The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER)
%END End position of the REF allele
%END0 End position of the REF allele in 0-based coordinates
%FIRST_ALT Alias for %ALT{0}
%FORMAT Prints all FORMAT fields or a subset of samples with -s or -S
%GT Genotype (e.g. 0/1)
%INFO Prints the whole INFO column
%INFO/TAG Any tag in the INFO column
%IUPACGT Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
%LINE Prints the whole line
%MASK Indicates presence of the site in other files (with multiple files)
%N_PASS(expr) Number of samples that pass the filtering expression (see *<<expressions,EXPRESSIONS>>*)
%POS0 POS in 0-based coordinates
%PBINOM(TAG) Calculate phred-scaled binomial probability, the allele index is determined from GT
%SAMPLE Sample name
%TAG{INT} Curly brackets to print a subfield (e.g. INFO/TAG{1}, the indexes are 0-based)
%TBCSQ Translated FORMAT/BCSQ. See the csq command above for explanation and examples.
%TGT Translated genotype (e.g. C/A)
%TYPE Variant type (REF, SNP, MNP, INDEL, BND, OTHER)
[] Format fields must be enclosed in brackets to loop over all samples
\n new line
\t tab character

Everything else is printed verbatim.

Examples:
# Print chromosome, position, ref allele and the first alternate allele
bcftools query -f '%CHROM %POS %REF %ALT{0}\n' file.vcf.gz

# Similar to above, but use tabs instead of spaces, add sample name and genotype
bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz

# Print FORMAT/GT fields followed by FORMAT/GT fields
bcftools query -f 'GQ:[ %GQ] \t GT:[ %GT]\n' file.vcf

# Make a BED file: chr, pos (0-based), end pos (1-based), id
bcftools query -f'%CHROM\t%POS0\t%END\t%ID\n' file.bcf

# Print only samples with alternate (non-reference) genotypes
bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf

# Print all samples at sites with at least one alternate genotype
bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]'

# Print phred-scaled binomial probability from FORMAT/AD tag for all heterozygous genotypes
bcftools query -i'GT="het"' -f'[%CHROM:%POS %SAMPLE %GT %PBINOM(AD)\n]' file.vcf

# Print the second value of AC field if bigger than 10. Note the (unfortunate) difference in
# index subscript notation: formatting expressions (-f) uses "{}" while filtering expressions
# (-i) use "[]". This is for historic reasons and backward-compatibility.
bcftools query -f '%AC{1}\n' -i 'AC[1]>10' file.vcf.gz

bcftools reheader [OPTIONS] file.vcf.gz
Modify header of VCF/BCF files, change sample names.

-f, --fai FILE
add to the header contig names and their lengths from the provided fasta index file
(.fai). Lengths of existing contig lines will be updated and contig lines not present
in the fai file will be removed

-h, --header FILE
new VCF header

-o, --output FILE
see Common Options

-s, --samples FILE
new sample names, one name per line, in the same order as they appear in the VCF file.
Alternatively, only samples which need to be renamed can be listed as "old_name
new_name\n" pairs separated by whitespaces, each on a separate line. If a sample name
contains spaces, the spaces can be escaped using the backslash character, for example
"Not\ a\ good\ sample\ name".

-T, --temp-prefix PATH
template for temporary file names, used with -f

--threads INT
see Common Options

bcftools roh [OPTIONS] file.vcf.gz
A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.

The HMM model:
Notation:
D = Data, AZ = autozygosity, HW = Hardy-Weinberg (non-autozygosity),
f = non-ref allele frequency

Transition probabilities:
tAZ = P(AZ|HW) .. from HW to AZ, the -a parameter
tHW = P(HW|AZ) .. from AZ to HW, the -H parameter

ci = P_i(C) .. probability of cross-over at site i, from genetic map
AZi = P_i(AZ) .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
HWi = P_i(HW)

P_{i+1}(AZ) = oAZ * max[(1 - tAZ * ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
P_{i+1}(HW) = oHW * max[(1 - tHW * ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]

General Options:
--AF-dflt FLOAT
in case allele frequency is not known, use the FLOAT. By default, sites where allele
frequency cannot be determined, or is 0, are skipped.

--AF-tag TAG
use the specified INFO tag TAG as an allele frequency estimate instead of the default
AC and AN tags. Sites which do not have TAG will be skipped.

--AF-file FILE
Read allele frequencies from a tab-delimited file containing the columns:
CHROM\tPOS\tREF,ALT\tAF. The file can be compressed with bgzip and indexed with tabix
-s1 -b2 -e2. Sites which are not present in the FILE or have different reference or
alternate allele will be skipped. Note that such a file can be easily created from a
VCF using:

bcftools query -f'%CHROM\t%POS\t%REF,%ALT\t%INFO/TAG\n' file.vcf | bgzip -c > freqs.tab.gz

-b, --buffer-size INT[,INT]
when the entire many-sample file cannot fit into memory, a sliding buffer approach can
be used. The first value is the number of sites to keep in memory. If negative, it is
interpreted as the maximum memory to use, in MB. The second, optional, value sets the
number of overlapping sites. The default overlap is set to roughly 1% of the buffer
size.

-e, --estimate-AF FILE
estimate the allele frequency by recalculating INFO/AC and INFO/AN on the fly, using
the specified TAG which can be either FORMAT/GT ("GT") or FORMAT/PL ("PL"). If TAG is
not given, "GT" is assumed. Either all samples ("-") or samples listed in FILE will be
included. For example, use "PL,-" to estimate AF from FORMAT/PL of all samples. If
neither -e nor the other --AF-... options are given, the allele frequency is estimated
from AC and AN counts which are already present in the INFO field.

--exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

-G, --GTs-only FLOAT
use genotypes (FORMAT/GT fields) ignoring genotype likelihoods (FORMAT/PL), setting PL
of unseen genotypes to FLOAT. Safe value to use is 30 to account for GT errors.

--include EXPRESSION
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.

-I, --skip-indels
skip indels as their genotypes are usually enriched for errors

-m, --genetic-map FILE
genetic map in the format required also by IMPUTE2. Only the first and third column
are used (position and Genetic_Map(cM)). The FILE can be a single file or a file mask,
where string "{CHROM}" is replaced with chromosome name.

-M, --rec-rate FLOAT
constant recombination rate per bp. In combination with --genetic-map, the --rec-rate
parameter is interpreted differently, as FLOAT-fold increase of transition
probabilities, which allows the model to become more sensitive yet still account for
recombination hotspots. Note that also the range of the values is therefore different
in both cases: normally the parameter will be in the range (1e-3,1e-9) but with
--genetic-map it will be in the range (10,1000).

-o, --output FILE
Write output to the FILE, by default the output is printed on stdout

-O, --output-type s|r[z]
Generate per-site output (s) or per-region output (r). By default both types are
printed and the output is uncompressed. Add z for a compressed output.

# Output fields:
RG = predicted homo/autozygous regions
- Sample
- Chromosome
- Start
- End
- Length (bp)
- Number of markers
- Quality .. average phred score in the region from the forward-backward algorithm

ST = per-site output showing:
- Sample
- Chromosome
- Position
- State .. predicted state from the Viterbi algorithm, 0 for normal (HW, Hardy-Weinberg) or 1 for autozygous (AZ)
- Quality .. quality score from the forward-backward algorithm

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

-s, --samples LIST
see Common Options

-S, --samples-file FILE
see Common Options

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

--targets-overlap 0|1|2
see Common Options

HMM Options:
-a, --hw-to-az FLOAT
P(AZ|HW) transition probability from AZ (autozygous) to HW (Hardy-Weinberg) state

-H, --az-to-hw FLOAT
P(HW|AZ) transition probability from HW to AZ state

-V, --viterbi-training FLOAT
estimate HMM parameters using Baum-Welch algorithm, using the convergence threshold
FLOAT, e.g. 1e-10 (experimental)

bcftools sort [OPTIONS] file.bcf
-m, --max-mem FLOAT[kMG]
Maximum memory to use. Approximate, affects the number of temporary files written to
the disk. Note that if the command fails at this step because of too many open files,
your system limit on the number of open files ("ulimit") may need to be increased.

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v[0-9]
see Common Options

-T, --temp-dir DIR
Use this directory to store temporary files

bcftools stats [OPTIONS] A.vcf.gz [B.vcf.gz]
Parses VCF or BCF and produces text file stats which is suitable for machine processing
and can be plotted using plot-vcfstats. When two files are given, the program generates
separate stats for intersection and the complements. By default only sites are compared,
-s/-S must given to include also sample columns. When one VCF file is specified on the
command line, then stats by non-reference allele frequency, depth distribution, stats by
quality and per-sample counts, singleton stats, etc. are printed. When two VCF files are
given, then stats such as concordance (Genotype concordance by non-reference allele
frequency, Genotype concordance by sample, Non-Reference Discordance) and correlation are
also printed. Per-site discordance (PSD) is also printed in --verbose mode.

--af-bins LIST|FILE
comma separated list of allele frequency bins (e.g. 0.1,0.5,1) or a file listing the
allele frequency bins one per line (e.g. 0.1\n0.5\n1)

--af-tag TAG
allele frequency INFO tag to use for binning. By default the allele frequency is
estimated from AC/AN, if available, or directly from the genotypes (GT) if not.

-1, --1st-allele-only
consider only the 1st alternate allele at multiallelic sites

-d, --depth INT,INT,INT
ranges of depth distribution: min, max, and size of the bin

--debug
produce verbose per-site and per-sample output

-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

-E, --exons file.gz
tab-delimited file with exons for indel frameshifts statistics. The columns of the
file are CHR, FROM, TO, with 1-based, inclusive, positions. The file is
BGZF-compressed and indexed with tabix

tabix -s1 -b2 -e3 file.gz

-f, --apply-filters LIST
see Common Options

-F, --fasta-ref ref.fa
faidx indexed reference sequence file to determine INDEL context

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.

-I, --split-by-ID
collect stats separately for sites which have the ID column set ("known sites") or
which do not have the ID column set ("novel sites").

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

-s, --samples LIST
see Common Options

-S, --samples-file FILE
see Common Options

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

--targets-overlap 0|1|2
see Common Options

-u, --user-tstv <TAG[:min:max:n]>
collect Ts/Tv stats for any tag using the given binning [0:1:100]

-v, --verbose
produce verbose per-site and per-sample output

bcftools view [OPTIONS] file.vcf.gz [REGION [...]]
View, subset and filter VCF or BCF files by position and filtering expression. Convert
between VCF and BCF. Former bcftools subset.

Output options
-G, --drop-genotypes
drop individual genotype information (after subsetting if -s option is set)

-h, --header-only
output the VCF header only (see also bcftools head)

-H, --no-header
suppress the header in VCF output

--with-header
output both VCF header and records (this is the default, but the option is useful for
explicitness or to reset the effects of -h or -H)

-l, --compression-level [0-9]
compression level. 0 stands for uncompressed, 1 for best speed and 9 for best
compression.

--no-version
see Common Options

-O, --output-type b|u|z|v[0-9]
see Common Options

-o, --output FILE: output file name. If not present, the default is to print to standard
output (stdout).

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--regions-overlap 0|1|2
see Common Options

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

--targets-overlap 0|1|2
see Common Options

--threads INT
see Common Options

Subset options:
-a, --trim-alt-alleles
remove alleles not seen in the genotype fields from the ALT column. Note that if no
alternate allele remains after trimming, the record itself is not removed but ALT is
set to ".". If the option -s or -S is given, removes alleles not seen in the subset.
INFO and FORMAT tags declared as Type=A, G or R will be trimmed as well.

--force-samples
only warn about unknown subset samples

-I, --no-update
do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)

-s, --samples LIST
see Common Options. Note that it is possible to create multiple subsets simultaneously
using the split plugin.

-S, --samples-file FILE
see Common Options. Note that it is possible to create multiple subsets simultaneously
using the split plugin.

Filter options:
Note that filter options below dealing with counting the number of alleles will, for
speed, first check for the values of AC and AN in the INFO column to avoid parsing all the
genotype (FORMAT/GT) fields in the VCF. This means that filters like --uncalled,
--exclude-uncalled', or --min-af 0.1 will be calculated from INFO/AC and INFO/AN when
available or FORMAT/GT otherwise. However, it will not attempt to use any other existing
field, like INFO/AF for example. For that, use --exclude AF<0.1 instead.

Also note that one must be careful when sample subsetting and filtering is performed in a
single command because the order of internal operations can influence the result. For
example, the -i/-e filtering is performed before sample removal, but the -P filtering is
performed after, and some are inherently ambiguous, for example allele counts can be taken
from the INFO column when present but calculated on the fly when absent. Therefore it is
strongly recommended to spell out the required order explicitly by separating such
commands into two steps. (Make sure to use the -O u option when piping!)

-c, --min-ac INT[:nref|:alt1|:minor|:major|:'nonmajor']
minimum allele count (INFO/AC) of sites to be printed. Specifying the type of allele
is optional and can be set to non-reference (nref, the default), 1st alternate
(alt1), the least frequent (minor), the most frequent (major) or sum of all but the
most frequent (nonmajor) alleles.

-C, --max-ac INT[:nref|:alt1|:minor|:'major'|:'nonmajor']
maximum allele count (INFO/AC) of sites to be printed. Specifying the type of allele
is optional and can be set to non-reference (nref, the default), 1st alternate
(alt1), the least frequent (minor), the most frequent (major) or sum of all but the
most frequent (nonmajor) alleles.

-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

-f, --apply-filters LIST
see Common Options

-g, --genotype [^][hom|het|miss]
include only sites with one or more homozygous (hom), heterozygous (het) or missing
(miss) genotypes. When prefixed with ^, the logic is reversed; thus ^het excludes
sites with heterozygous genotypes.

-i, --include EXPRESSION
include sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

-k, --known
print known sites only (ID column is not ".")

-m, --min-alleles INT
print sites with at least INT alleles listed in REF and ALT columns

-M, --max-alleles INT
print sites with at most INT alleles listed in REF and ALT columns. Use -m2 -M2 -v
snps to only view biallelic SNPs.

-n, --novel
print novel sites only (ID column is ".")

-p, --phased
print sites where all samples are phased. Haploid genotypes are considered phased.
Missing genotypes considered unphased unless the phased bit is set.

-P, --exclude-phased
exclude sites where all samples are phased

-q, --min-af FLOAT[:nref|:alt1|:minor|:major|:nonmajor]
minimum allele frequency (INFO/AC / INFO/AN) of sites to be printed. Specifying the
type of allele is optional and can be set to non-reference (nref, the default), 1st
alternate (alt1), the least frequent (minor), the most frequent (major) or sum of all
but the most frequent (nonmajor) alleles.

-Q, --max-af FLOAT[:nref|:alt1|:minor|:major|:nonmajor]
maximum allele frequency (INFO/AC / INFO/AN) of sites to be printed. Specifying the
type of allele is optional and can be set to non-reference (nref, the default), 1st
alternate (alt1), the least frequent (minor), the most frequent (major) or sum of all
but the most frequent (nonmajor) alleles.

-u, --uncalled
print sites without a called genotype, i.e. print sites with all genotypes missing.
Note that the missingness is determined from INFO/AN and AC tags when available to
avoid parsing sample fields.

-U, --exclude-uncalled
exclude sites without a called genotype, i.e. print sites with at least one
non-missing genotype. Note that the missingness is determined from INFO/AN and AC tags
when available to avoid parsing sample fields.

-v, --types snps|indels|mnps|other
comma-separated list of variant types to select. Site is selected if any of the ALT
alleles is of the type requested. Types are determined by comparing the REF and ALT
alleles in the VCF record not INFO tags like INFO/INDEL or INFO/VT. Use --include to
select based on INFO tags.

-V, --exclude-types snps|indels|mnps|ref|bnd|other
comma-separated list of variant types to exclude. Site is excluded if any of the ALT
alleles is of the type requested. Types are determined by comparing the REF and ALT
alleles in the VCF record not INFO tags like INFO/INDEL or INFO/VT. Use --exclude to
exclude based on INFO tags.

-x, --private
print sites where only the subset samples carry an non-reference allele. Requires
--samples or --samples-file.

-X, --exclude-private
exclude sites where only the subset samples carry an non-reference allele

bcftools help [COMMAND] | bcftools --help [COMMAND]
Display a brief usage message listing the bcftools commands available. If the name of a
command is also given, e.g., bcftools help view, the detailed usage message for that
particular command is displayed.

bcftools [--version|-v]
Display the version numbers and copyright information for bcftools and the important
libraries used by bcftools.

bcftools [--version-only]
Display the full bcftools version number in a machine-readable format.

EXPRESSIONS

       These filtering expressions are accepted by most of the commands.

       Valid expressions may contain:

       •   numerical constants, string constants, file names (this is currently supported only to
           filter by the ID column)

               1, 1.0, 1e-4
               "String"
               @file_name

       •   arithmetic operators (addition, multiplication, subtraction, division, modulo)

               +, *, -, /, %

       •   comparison operators

               == (same as =), >, >=, <=, <, !=

       •   regex operators "\~" and its negation "!~". The expressions are case sensitive unless
           "/i" is added.

               INFO/HAYSTACK ~ "needle"
               INFO/HAYSTACK ~ "NEEDless/i"

       •   parentheses

               (, )

       •   logical operators. See also the examples below and the filtering tutorial
           <http://samtools.github.io/bcftools/howtos/filtering.html> about the distinction
           between "&&" vs "&" and "||" vs "|".

               &&,  &, ||,  |

       •   INFO tags, FORMAT tags, column names

               INFO/DP or DP
               FORMAT/DV, FMT/DV, or DV
               FILTER, QUAL, ID, CHROM, POS, REF, ALT[0]

       •   the FILTER column can be queried as follows:

               FILTER="PASS"
               FILTER="."
               FILTER="A"          .. exact match, for example "A;B" does not pass
               FILTER="A;B"        .. exact match, "A;B" and "B;A" pass, everything else fails
               FILTER!="A"         .. exact match, for example "A;B" does pass
               FILTER~"A"          .. subset match, for example both "A" and "A;B" pass
               FILTER~"A;B"        .. subset match, pass only if both "A" and "B" are present
               FILTER!~"A"         .. complement match, for example both "A" and "A;B" fail
               FILTER!~"A;B"       .. complement match, fail if both "A" and "B" are present

       •   1 (or 0) to test the presence (or absence) of a flag

               FlagA=1 && FlagB=0

       •   "." to test missing values

               DP=".", DP!=".", ALT="."

       •   missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".",
           "0|.") using these expressions

               GT="mis", GT~"\.", GT!~"\."

       •   missing genotypes can be matched including the phase and ploidy (".|.", "./.", ".")
           using these expressions

               GT=".|.", GT="./.", GT="."

       •   sample genotype: reference (haploid or diploid), alternate (hom or het, haploid or
           diploid), missing genotype, homozygous, heterozygous, haploid, ref-ref hom, alt-alt
           hom, ref-alt het, alt-alt het, haploid ref, haploid alt (case-insensitive)

               GT="ref"
               GT="alt"
               GT="mis"
               GT="hom"
               GT="het"
               GT="hap"
               GT="RR"
               GT="AA"
               GT="RA" or GT="AR"
               GT="Aa" or GT="aA"
               GT="R"
               GT="A"

       •   TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,bnd,other,overlap). Use
           the regex operator "\~" to require at least one allele of the given type or the equal
           sign "=" to require that all alleles are of the given type. Compare

               TYPE="snp"
               TYPE~"snp"
               TYPE!="snp"
               TYPE!~"snp"

       •   array subscripts (0-based), "*" for any element, "-" to indicate a range. Note that
           for querying FORMAT vectors, the colon ":" can be used to select a sample and an
           element of the vector, as shown in the examples below.

               INFO/AF[0] > 0.3             .. first AF value bigger than 0.3
               FORMAT/AD[0:0] > 30          .. first AD value of the first sample bigger than 30
               FORMAT/AD[0:1]               .. first sample, second AD value
               FORMAT/AD[1:0]               .. second sample, first AD value
               DP4[*] == 0                  .. any DP4 value
               FORMAT/DP[0]   > 30          .. DP of the first sample bigger than 30
               FORMAT/DP[1-3] > 10          .. samples 2-4
               FORMAT/DP[1-]  < 7           .. all samples but the first
               FORMAT/DP[0,2-4] > 20        .. samples 1, 3-5
               FORMAT/AD[0:1]               .. first sample, second AD field
               FORMAT/AD[0:*], AD[0:] or AD[0] .. first sample, any AD field
               FORMAT/AD[*:1] or AD[:1]        .. any sample, second AD field
               (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
               CSQ[*] ~ "missense_variant.*deleterious"

       •   in addition to array subscripts shown above, it is possible to subscript arrays of
           Number=R tags by alleles found in FORMAT/GT (starting with version 1.17). For example

               FORMAT/AD[GT] > 10        .. require support of more than 10 reads for each allele
               FORMAT/AD[0:GT] > 10      .. same as above, but in the first sample
               sSUM(FORMAT/AD[GT]) > 20  .. require total sample depth bigger than 20

       •   with many samples it can be more practical to provide a file with sample names, one
           sample name per line

               GT[@samples.txt]="het" & binom(AD)<0.01

       •   function on FORMAT tags (over samples) and INFO tags (over vector fields): maximum;
           minimum; arithmetic mean (AVG is synonymous with MEAN); median; standard deviation
           from mean; sum; string length; absolute value; number of elements:

               MAX, MIN, AVG, MEAN, MEDIAN, STDEV, SUM, STRLEN, ABS, COUNT

           Note that functions above evaluate to a single value across all samples and are
           intended to select sites, not samples, even when applied on FORMAT tags. However, when
           prefixed with SMPL_ (or "s" for brevity, e.g. SMPL_MAX or sMAX), they will evaluate to
           a vector of per-sample values when applied on FORMAT tags:

               SMPL_MAX, SMPL_MIN, SMPL_AVG, SMPL_MEAN, SMPL_MEDIAN, SMPL_STDEV, SMPL_SUM,
               sMAX, sMIN, sAVG, sMEAN, sMEDIAN, sSTDEV, sSUM

       •   two-tailed binomial test. Note that for N=0 the test evaluates to a missing value and
           when FORMAT/GT is used to determine the vector indices, it evaluates to 1 for
           homozygous genotypes.

               binom(FMT/AD)                .. GT can be used to determine the correct index
               binom(AD[0],AD[1])           .. or the fields can be given explicitly
               phred(binom())               .. the same as binom but phred-scaled

       •   variables calculated on the fly if not present: number of alternate alleles; number of
           samples; count of alternate alleles; minor allele count (similar to AC but is always
           smaller than 0.5); frequency of alternate alleles (AF=AC/AN); frequency of minor
           alleles (MAF=MAC/AN); number of alleles in called genotypes; number of samples with
           missing genotype; fraction of samples with missing genotype; indel length (deletions
           negative, insertions positive)

               N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN, N_MISSING, F_MISSING, ILEN

       •   the number (N_PASS) or fraction (F_PASS) of samples which pass the expression

               N_PASS(GQ>90 & GT!="mis") > 90
               F_PASS(GQ>90 & GT!="mis") > 0.9

       •   custom perl filtering. Note that this command is not compiled in by default, see the
           section Optional Compilation with Perl in the INSTALL file for help and
           misc/demo-flt.pl for a working example. The demo defined the perl subroutine
           "severity" which can be invoked from the command line as follows:

               perl:path/to/script.pl; perl.severity(INFO/CSQ) > 3

       Notes:

       •   String comparisons and regular expressions are case-insensitive

       •   Comma in strings is interpreted as a separator and when multiple values are compared,
           the OR logic is used. Consequently, the following two expressions are equivalent but
           not the third:

               -i 'TAG="hello,world"'
               -i 'TAG="hello" || TAG="world"'
               -i 'TAG="hello" && TAG="world"'

       •   Variables and function names are case-insensitive, but not tag names. For example,
           "qual" can be used instead of "QUAL", "strlen()" instead of "STRLEN()" , but not "dp"
           instead of "DP".

       •   When querying multiple values, all elements are tested and the OR logic is used on the
           result. For example, when querying "TAG=1,2,3,4", it will be evaluated as follows:

               -i 'TAG[*]=1'   .. true, the record will be printed
               -i 'TAG[*]!=1'  .. true
               -e 'TAG[*]=1'   .. false, the record will be discarded
               -e 'TAG[*]!=1'  .. false
               -i 'TAG[0]=1'   .. true
               -i 'TAG[0]!=1'  .. false
               -e 'TAG[0]=1'   .. false
               -e 'TAG[0]!=1'  .. true

       •   When arithmetic operators are used on vectors A and B, the following logic is used to
           compute the resulting vector C:

           •   C_i = A_i + B_i when length(A)==B(A) and sets length©=length(A)

           •   C_i = A_i + B_0 when length(B)=1 and sets length©=length(A)

           •   C_i = A_0 + B_i when length(A)=1 and sets length©=length(B)

           •   throw an error when length(A)!=length(B) AND length(A)!=1 AND length(B)!=1

       Examples:

           MIN(DV)>5       .. selects the whole site, evaluates min across all values and samples

           SMPL_MIN(DV)>5  .. selects matching samples, evaluates within samples

           MIN(DV/DP)>0.3

           MIN(DP)>10 & MIN(DV)>3

           FMT/DP>10  & FMT/GQ>10 .. both conditions must be satisfied within one sample

           FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples

           QUAL>10 |  FMT/GQ>10   .. true for sites with QUAL>10 or a sample with GQ>10, but selects only samples with GQ>10

           QUAL>10 || FMT/GQ>10   .. true for sites with QUAL>10 or a sample with GQ>10, plus selects all samples at such sites

           TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)

           COUNT(GT="hom")=0      .. no homozygous genotypes at the site

           AVG(GQ)>50             .. average (arithmetic mean) of genotype qualities bigger than 50

           ID=@file       .. selects lines with ID present in the file

           ID!=@~/file    .. skip lines with ID present in the ~/file

           MAF[0]<0.05    .. select rare variants at 5% cutoff

           POS>=100   .. restrict your range query, e.g. 20:100-200 to strictly sites with POS in that range.

       Shell expansion:

       Note that expressions must often be quoted because some characters have special meaning in
       the shell. An example of expression enclosed in single quotes which cause that the whole
       expression is passed to the program as intended:

           bcftools view -i '%ID!="." & MAF[0]<0.01'

       Please refer to the documentation of your shell for details.

SCRIPTS AND OPTIONS

plot-vcfstats [OPTIONS] file.vchk [...]
Script for processing output of bcftools stats. It can merge results from multiple outputs
(useful when running the stats for each chromosome separately), plots graphs and creates a
PDF presentation.

-m, --merge
Merge vcfstats files to STDOUT, skip plotting.

-p, --prefix DIR
The output directory. This directory will be created if it does not exist.

-P, --no-PDF
Skip the PDF creation step.

-r, --rasterize
Rasterize PDF images for faster rendering. This is the default and the opposite of -v,
--vectors.

-s, --sample-names
Use sample names for xticks rather than numeric IDs.

-t, --title STRING
Identify files by these titles in plots. The option can be given multiple times, for
each ID in the bcftools stats output. If not present, the script will use abbreviated
source file names for the titles.

-v, --vectors
Generate vector graphics for PDF images, the opposite of -r, --rasterize.

-T, --main-title STRING
Main title for the PDF.

Example:

# Generate the stats
bcftools stats -s - > file.vchk

# Plot the stats
plot-vcfstats -p outdir file.vchk

# The final looks can be customized by editing the generated
# 'outdir/plot.py' script and re-running manually
cd outdir && python plot.py && pdflatex summary.tex

PERFORMANCE

       HTSlib was designed with BCF format in mind. When parsing VCF files, all records are
       internally converted into BCF representation. Simple operations, like removing a single
       column from a VCF file, can be therefore done much faster with standard UNIX commands,
       such as awk or cut. Therefore it is recommended to use BCF as input/output format whenever
       possible to avoid large overhead of the VCF → BCF → VCF conversion.

BUGS

       Please report any bugs you encounter on the github website:
       http://github.com/samtools/bcftools

AUTHORS

       Heng Li from the Sanger Institute wrote the original C version of htslib, samtools and
       bcftools. Bob Handsaker from the Broad Institute implemented the BGZF library. Petr
       Danecek, Shane McCarthy and John Marshall are  maintaining and further developing
       bcftools. Many other people contributed to the program and to the file format
       specifications, both directly and indirectly by providing patches, testing and reporting
       bugs. We thank them all.

RESOURCES

       BCFtools GitHub website: http://github.com/samtools/bcftools

       Samtools GitHub website: http://github.com/samtools/samtools

       HTSlib GitHub website: http://github.com/samtools/htslib

       File format specifications: http://samtools.github.io/hts-specs

       BCFtools documentation: http://samtools.github.io/bcftools

       BCFtools wiki page: https://github.com/samtools/bcftools/wiki

COPYING

       The MIT/Expat License or GPL License, see the LICENSE document for details. Copyright (c)
       Genome Research Ltd.

                                            2023-02-21                                BCFTOOLS(1)