Provided by: bcftools_1.2-2_amd64 bug

NAME

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

SYNOPSIS

       bcftools [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.

       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 2015-03-20 11:57 GMT and refers to bcftools git version
       1.2-6-ga8d7fe9+.

   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")

       ·    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

       ·    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

       ·    norm .. normalize indels

       ·    plugin .. run user-defined plugin

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

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

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

       ·    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.

       -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).

       -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. 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 "^".

       -S, --samples-file FILE
           File of sample names to include or exclude if prefixed with "^". One sample per line.
           The command bcftools call accepts an optional second column indicating ploidy (0, 1 or
           2) and can parse also PED files. With bcftools call -C trio, PED file is expected.

       -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. Such a file can
           be easily created from a VCF using:

               bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf

   bcftools annotate [OPTIONS] FILE
       This command allows one to 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.

       -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". 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 values without
           overwriting existing annotations, use "+TAG" instead of "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.

       -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.

       -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:
           -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, --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

       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.

           -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.

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

           -o, --output FILE
               see Common Options

           -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.

           -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 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.

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

       -D, --remove-duplicates
           If a record is present in multiple files, output only the first instance. Requires -a,
           --allow-overlaps.

       -f, --file-list FILE
           Read the list of files from a file.

       -l, --ligate
           Ligate phased VCFs by matching phase at overlapping haplotypes

       -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.

   bcftools consensus [OPTIONS] FILE
       Create consensus sequence by applying VCF variants to a reference fasta file.

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

       -H, --haplotype 1|2
           apply variants for the given haplotype. This option requires -s, unless exactly one
           sample is present in the VCF

       -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:
           -o, --output FILE
               see Common Options

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

       gVCF conversion:
           --gvcf2vcf
               convert gVCF to VCF, expanding REF blocks into sites. Only sites with FILTER set
               to "PASS" or "." will be expanded.

       HAPS/SAMPLE conversion:
           --hapsample2vcf prefix or haps-file,sample-file
               convert from haps/sample format to VCF. The columns of .haps file are similar to
               .gen file above, but there are only two haplotype columns per sample. Note that
               the first column of the haps file is expected to be in the form "CHR:POS_REF_ALT",
               for example:

                 .haps
                 ----
                 1:111485207_G_A rsID1 111485207 G A 0 1 0 0
                 1:111494194_C_T rsID2 111494194 C T 0 1 0 0

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

           -h, --haplegendsample prefix or haps-file,legend-file,sample-file
               convert from VCF to haps/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:

                 .haps
                 -----
                 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.

           --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

           -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 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.

       -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

   bcftools gtcheck [OPTIONS] [-g genotypes.vcf.gz] query.vcf.gz
       Checks sample identity or, without -g, multi-sample cross-check is performed.

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

       -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.

           SM, Average Discordance
               Average discordance between sample a and all other samples.

           SM, Average Depth
               Average depth at evaluated sites, or 1 if FORMAT/DP field is not present.

           SM, Average Number of sites
               The average number of sites used to calculate the discordance. In other words, the
               average number of non-missing PLs/genotypes seen both samples.

   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

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

       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
           output positions present in this many (=), this many or more (+), or this many or
           fewer (-) 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

   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

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

       -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.

       -l, --file-list FILE
           read file names from FILE

       -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

       -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

   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.

       -D, --remove-duplicates
           remove duplicate lines of the same type

       -f, --fasta-ref FILE
           reference sequence

       -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.

       -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

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

   bcftools plugin NAME [OPTIONS] FILE[PLUGIN OPTIONS]
       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:
           -o, --output FILE
               see Common Options

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

               If htslib is not installed systemwide, set the environment variable
               LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include the directory
               where libhts.so.1 is located.

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

       List of plugins coming with the distribution:
           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.

           fix-ploidy
               sets correct ploidy

           frameshifts
               annotate frameshift indels

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

           tag2tag
               Convert between similar tags, such as GL and GP.

           vcf2sex
               determine sample sex by checking genotypes in haploid regions

       Examples:
               # List options common to all plugins
               bcftools plugin

               # List available plugins
               bcftools plugin -l

               # One can run plugins in several ways
               bcftools plugin counts in.vcf
               bcftools +counts in.vcf
               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?

           ·   Are all shared libraries, namely libhts.so, accessible? Verify with

               ·   on Mac OS X: otool -L your/plugin.so and set DYLD_LIBRARY_PATH if they are not

               ·   on Linux: ldd your/plugin.so and set LD_LIBRARY_PATH if they are not

           ·   If not installed systemwide, set the environment variable LD_LIBRARY_PATH (linux)
               or DYLD_LIBRARY_PATH (mac) to include directory where libhts.so is located.

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

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

       -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

       -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, 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}
               []              The brackets loop over all samples
               %GT             Genotype (e.g. 0/1)
               %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

       Examples:
               bcftools query -f '%CHROM  %POS  %REF  %ALT{0}\n' file.vcf.gz
               bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz

   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 separate line.

   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
                 P(AZ|AZ) = 1 - P(HW|AZ) = 1 - tHW
                 P(HW|HW) = 1 - P(AZ|HW) = 1 - tAZ

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

       General Options:
           --AF-tag TAG
               use the specified INFO tag TAG as an allele frequency estimate instead of the
               defaul 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

           -e, --estimate-AF FILE
               recalculate INFO/AC and INFO/AN on the fly, using either all samples ("-") or
               samples listed in FILE. By default, allele frequency is estimated from AC and AN
               counts which are already present in the INFO field.

           -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.

           -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.

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

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

           -s, --sample name
               the name of sample to analyze

           -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
               perform Viterbi training to estimate transition probabilities

   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.

       -1, --1st-allele-only
           consider only 1st 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, --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, --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

   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.

           -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

       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

           -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:
           -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

           -V, --exclude-types snps|indels|mnps|other
               comma-separated list of variant types to exclude

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

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

EXPRESSIONS

       These filtering expressions are accepted by annotate, filter, query and view 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 "!~"

               INFO/HAYSTACK ~ "needle"

       ·   parentheses

               (, )

       ·   logical operators

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

       ·   INFO tags, FORMAT tags, column names

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

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

               FlagA=1 && FlagB=0

       ·   TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)

               TYPE="indel" | TYPE="snp"

       ·   array subscripts, "*" for any field

               (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
               DP4[*] == 0
               CSQ[*] ~ "missense_variant.*deleterious"

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

               MAX, MIN, AVG, SUM, STRLEN, ABS

       ·   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

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

       Notes:

       ·   String comparisons and regular expressions are case-insensitive

       ·   If the subscript "*" is used in regular expression search, the whole field is treated
           as one string. For example, the regex STR[*]~"B,C" will be true for the string vector
           INFO/STR=AB,CD.

       ·   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".

       Examples:

           MIN(DV)>5

           MIN(DV/DP)>0.3

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

           QUAL>10 |  FMT/GQ>10   .. selects only GQ>10 samples

           QUAL>10 || FMT/GQ>10   .. selects all samples at QUAL>10 sites

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

           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

       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 PATH
           The output files prefix, add a slash to create new directory.

       -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.

                                       2015-03-20 11:57 GMT                           BCFTOOLS(1)