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 2019-12-19 and refers to bcftools git version 1.10.2.

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

• 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.

-O, --output-type b|u|z|v
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.

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
Comma-separated list of regions, see also -R, --regions-file. 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 are: CHROM, POS, and,
optionally, POS_TO, where positions are 1-based and inclusive. The columns of the
tab-delimited BED file are also CHROM, POS and POS_TO (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.

-s, --samples [^]LIST
Comma-separated list of samples to include or exclude if prefixed with "^". 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 two is that -r checks both start and end
positions of indels, whereas -t checks start positions only. 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 index. 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. 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. 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
# etc.

-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.

To add annotations without overwriting existing values (that is, to add missing tags
or add values to existing tags with missing values), use "+TAG" instead of "TAG". 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".

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.

-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|unique|sum|avg|min|max[,...]
if multiple regions overlap a single record, the 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
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 if BEG and END --columns are present.

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

--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
see Common Options

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

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

--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

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, 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
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

-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

--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.

-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 FORMAT/AD generated at the bcftools mpileup step
by providing the -a FMT/AD option.

-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

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

-t, --targets LIST
see Common Options

-T, --targets-file FILE
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|none
Output duplicate records of specified type present in multiple files only once.
Requires -a, --allow-overlaps.

-D, --remove-duplicates
Alias for -d none

-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 other are dropped.

--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
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.

--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.

-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|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)

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

-m, --mask FILE
BED file or TAB file with regions to be replaced with N. See discussion of
--regions-file in Common Options for file format details.

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

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

-s, --sample NAME
apply variants of the given sample

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".
samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz -o out.fa

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

-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

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

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
see Common Options

--threads INT
see Common Options

GEN/SAMPLE conversion:
-G, --gensample2vcf prefix or gen-file,sample-file
convert IMPUTE2 output to VCF. The second column must be of the form
"CHROM:POS_REF_ALT" to detect possible strand swaps; IMPUTE2 leaves the first one
empty ("--") when sites from reference panel are filled in. See also -g below.

-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". For example:

.gen
----
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

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

--chrom
output chromosome in the first column instead of CHROM:POS_REF_ALT

--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 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
----
1:111485207_G_A rsID1 111485207 G A 0 1 0 0
1:111494194_C_T rsID2 111494194 C T 0 1 0 0
1:111495231_A_<DEL>_111495784 rsID3 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
output VCF IDs instead of "CHROM:POS_REF_ALT" IDs

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" IDs

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 in the FORMAT/BCSQ tags. By default this is 16, 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, --brief-predictions
annotate with abbreviated protein-changing predictions. That is, instead of writing
the whole modified protein sequence with potentially hundreds of aminoacids, 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 consequences to consider per 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 16 which corresponds to one integer per diploid sample. Note that
increasing the value leads to increased memory and is rarely necessary.

--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|t|u|z|v
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

-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

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

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
filter SNPs within INT base pairs of an indel. 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.

-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
see Common Options

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

-R, --regions-file file
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

--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 the -s sample 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.

-a, --all-sites
output for all sites

-c, --cluster FLOAT,FLOAT
min inter- and max intra-sample error [0.23,-0.3]

The first "min" argument controls the typical error rate in multiplexed
runs ("lanelets") from the same sample. Lanelets with error rate less
than this will always be considered as coming from the same sample.
The second "max" argument is the reverse: lanelets with error rate
greater than the absolute value of this parameter will always be
considered as different samples. When the value is negative, the cutoff
may be heuristically lowered by the clustering engine. If positive, the
value is interpreted as a fixed cutoff.

-g, --genotypes genotypes.vcf.gz
reference genotypes to compare against

-G, --GTs-only INT
use genotypes (GT) instead of genotype likelihoods (PL). When set to 1, reported
discordance is the number of non-matching GTs, otherwise the number INT is interpreted
as phred-scaled likelihood of unobserved genotypes.

-H, --homs-only
consider only genotypes which are homozygous in both genotypes and query VCF. This may
be useful with low coverage data.

-p, --plot PREFIX
produce plots

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

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

-s, --query-sample STRING
query sample in query.vcf.gz. By default, the first sample is checked.

-S, --target-sample STRING
target sample in the -g file, used only for plotting, not for analysis

-t, --targets file
see Common Options

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

Output files format:
CN, Discordance
Pairwise discordance for all sample pairs is calculated as

\sum_s { min_G { PL_a(G) + PL_b(G) } },

where the sum runs over all sites s and G is the the most likely genotype shared
by both samples a and b. When PL field is not present, a constant value 99 is used
for the unseen genotypes. With -G, the value 1 can be used instead; the
discordance value then gives exactly the number of differing genotypes.

ERR, error rate
Pairwise error rate calculated as number of differences divided by the total
number of comparisons.

CLUSTER, TH, DOT
In presence of multiple samples, related samples and outliers can be identified by
clustering samples by error rate. A simple hierarchical clustering based on
minimization of standard deviation is used. This is useful to detect sample swaps,
for example in situations where one sample has been sequenced in multiple runs.

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 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:
-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.

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
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

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

-T, --targets-file file
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 four 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.

-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 id .. merge by ID

--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
see Common Options

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

-R, --regions-file file
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 disables this functionality; if enabled, the recommended value for BWA
is 50. [0]

-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

-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]

-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

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

--rf, --incl-flags STR|INT
Required flags: skip reads with mask bits unset [null]

--ff, --excl-flags STR|INT
Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]

-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

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

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
see Common Options

--threads INT
see Common Options

Options for SNP/INDEL genotype likelihood computation
-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 [100]

-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]

-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.

-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.)

-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.

--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

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
see Common Options

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

-R, --regions-file file
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

--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

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

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

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

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
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 INFO tags AF, AC, AC_Hemi, AC_Hom, AC_Het, AN, ExcHet, HWE, MAF, NS

fix-ploidy
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.

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 or linkage disequilibrium

remove-overlaps
remove overlapping variants and duplicate sites

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-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 and GP

trio-dnm
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

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

# 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

-s, --sample string
sample name

-t, --targets LIST
see Common Options

-T, --targets-file FILE
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.

-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

-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

-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)
%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".

--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 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.

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

-R, --regions-file file
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

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
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

-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

-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

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

-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
see Common Options

-o, --output-file 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

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

-T, --targets-file file
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

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

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 a filter like --min-af 0.1
will be based ‘AC/AN’ where AC and AN come from either INFO/AC and INFO/AN if
available or FORMAT/GT if not. It will not filter on another field like INFO/AF. The
--include and --exclude filter expressions should instead be used to explicitly filter
based on fields in the INFO column, e.g. --exclude AF<0.1.

-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

-U, --exclude-uncalled
exclude sites without a called genotype

-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

               +,*,-,/

       •   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 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]

       •   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 (".|.", "./.", ".")
           using these expressions

               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"

       •   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;
           sum; string length; absolute value; number of elements (matching columns for FORMAT
           tags or number of fields for INFO tags).

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

       •   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

       •   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

       Examples:

           MIN(DV)>5

           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.

                                            2019-12-19                                BCFTOOLS(1)