bcftools

## 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 2015-01-21 15:01 GMT and refers to bcftools git version 1.1-140-g9b0e7cc+.

### 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 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 explictly 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. If not installed systemwide, set the environment variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include directory where libhts.so is located. The BCFTOOLS_PLUGINS environment variable tells the program which directories to search.
-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 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.