Provided by: bcftools_1.8-1_amd64 bug

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.

       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 2018-04-03 and refers to bcftools git version 1.8.

   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"), and can parse also PED files. If the second column is not
           present, the sex "F" is assumed. With bcftools call -C trio, PED file is expected.
           File formats examples:

               sample1    1
               sample2    2
               sample3    2

             or

               sample1    M
               sample2    F
               sample3    F

             or a .ped file (here is shown a minimum working example, the first column is
             ignored and the last indicates sex: 1=male, 2=female)

               ignored daughterA fatherA motherA 2
               ignored 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
           Number of output compression threads to use in addition to main thread. Only used 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. 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.

       --collapse snps|indels|both|all|some|none
           Controls how to match records from the annotation file to the target VCF. Effective
           only when -a is a VCF or BCF. See Common Options for more.

       -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.

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

       -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 wich do not pass -i and -e expressions instead of discarding them

       -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.

       --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 inut.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-AN-AC plugin
                   bcftools +fill-AN-AC 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, --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 modelfor 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 samply 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 but dangerous if the
       BCF headers differ.

       -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

       --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 implicit
           order of the contig and tag definitions in the header. Currently no sanity checks are
           in place. 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
           choose which allele from the FORMAT/GT field to use (the codes are case-insensitive):

           1
               the first allele

           2
               the second allele

           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)

                   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.

       -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. Only sites with FILTER set
               to "PASS" or "." will be expanded.

           -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

           --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

       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 contruction 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

       -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)

       -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.

       -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 consquences 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

               # A frame-restoring combination of two frameshift insertions C>CG and T>TGG
               BCSQ=@46115084
               BCSQ=inframe_insertion|COPZ2|ENST00000006101|-|18AGRGP>18AQAGGP|46115072C>CG+46115084T>TGG

               # 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, --collapse snps|indels|both|all|some|none
           see Common Options

       -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 and B (but not in C) and create intersection

                   bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e- A.vcf.gz B.vcf.gz C.vcf.gz -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 norm instead.

       --force-samples
           if the merged files contain duplicate samples names, proceed anyway. Duplicate sample
           names will be resolved by prepending 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, --merge snps|indels|both|all|none|id
           The option controls what types of multiallelic records can be created:

           -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 posi- tion, 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 bcftools has a
               minimum value of 8000/n where n is the number of input files given to mpileup.
               This means the default is highly likely to be increased. Once above the
               cross-sample minimum of 8000 the -d parameter will have an effect. [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)

                   *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)

                   *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.

       -d, --rm-dup snps|indels|both|all|none
           If a record is present multiple times, output only the first instance, see --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.

       -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:
           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

           ad-bias
               find positions with wildly varying ALT allele frequency (Fisher test on FMT/AD)

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

           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

           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-AN-AC
               fill INFO fields AN and AC.

           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, HWE, MAF, NS

           fix-ploidy
               sets correct ploidy

           fixref
               determine and fix strand orientation

           frameshifts
               annotate frameshift indels

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

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

           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")

           prune
               prune sites by missingness or linkage disequilibrium

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

           tag2tag
               convert between similar tags, such as GL and GP

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

       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)
               %INFO/TAG       Any tag in the INFO column
               %TYPE           Variant type (REF, SNP, MNP, INDEL, BND, OTHER)
               %MASK           Indicates presence of the site in other files (with multiple files)
               %TAG{INT}       Curly brackets to subscript vectors (0-based)
               %FIRST_ALT      Alias for %ALT{0}
               []              Format fields must be enclosed in brackets to loop over all samples
               %GT             Genotype (e.g. 0/1)
               %TBCSQ          Translated FORMAT/BCSQ. See the csq command above for explanation and examples.
               %TGT            Translated genotype (e.g. C/A)
               %IUPACGT        Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
               %LINE           Prints the whole line
               %SAMPLE         Sample name
               %POS0           POS in 0-based coordinates
               %END            End position of the REF allele
               %END0           End position of the REF allele in 0-based cordinates
               \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]'

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

       -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".

   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

               Emission probabilities:
                 oAZ = P_i(D|AZ) = (1-f)*P(D|RR) + f*P(D|AA)
                 oHW = P_i(D|HW) = (1-f)^2 * P(D|RR) + f^2 * P(D|AA) + 2*f*(1-f)*P(D|RA)

               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

       -c, --collapse snps|indels|both|all|some|none
           see Common Options

       -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
               trim alternate alleles not seen in subset. Type A, G and R INFO and FORMAT fields
               will also be trimmed

           --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

               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

               && (same as &), ||,  |

       ·   INFO tags, FORMAT tags, column names

               INFO/DP or DP
               FORMAT/DV, FMT/DV, or DV
               FILTER, QUAL, ID, 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). 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"

       ·   function on FORMAT tags (over samples) and INFO tags (over vector fields)

               MAX, MIN, AVG, SUM, STRLEN, ABS, COUNT

       ·   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

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

       ·   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

           MIN(DP)>35 && AVG(GQ)>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.

       -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.

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

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.

                                            2018-04-03                                BCFTOOLS(1)