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bcftools(1)
===========
:doctype: manpage


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 *{date}* and refers to bcftools git version *{version}*.

=== 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,annotate>>*   .. edit VCF files, add or remove annotations
- *<<call,call>>*        ..  SNP/indel calling (former "view")
- *<<concat,concat>>*    ..  concatenate VCF/BCF files from the same set of samples
- *<<consensus,consensus>>*    ..  create consensus sequence by applying VCF variants
- *<<convert,convert>>*  ..  convert VCF/BCF to other formats and back
- *<<filter,filter>>*    ..  filter VCF/BCF files using fixed thresholds
- *<<gtcheck,gtcheck>>*  ..  check sample concordance, detect sample swaps and contamination
- *<<index,index>>*      ..  index VCF/BCF
- *<<isec,isec>>*        ..  intersections of VCF/BCF files
- *<<merge,merge>>*      ..  merge VCF/BCF files files from non-overlapping sample sets
- *<<norm,norm>>*        ..  normalize indels
- *<<plugin,plugin>>*    ..  run user-defined plugin
- *<<query,query>>*      ..  transform VCF/BCF into user-defined formats
- *<<reheader,reheader>>*   ..  modify VCF/BCF header, change sample names
- *<<roh,roh>>*          ..  identify runs of homo/auto-zygosity
- *<<stats,stats>>*      ..  produce VCF/BCF stats (former vcfcheck)
- *<<view,view>>*        ..  subset, filter and convert VCF and BCF files


LIST OF SCRIPTS
---------------
Some helper scripts are bundled with the bcftools code.

- *<<plot-vcfstats,plot-vcfstats>>*  .. plots the output of *<<stats,stats>>*


COMMANDS AND OPTIONS
--------------------

[[common_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'{nbsp} *-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'{nbsp} *-c* 'snps'"

        'id';;
            only records with identical ID column are compatible.
            Supported by *<<merge,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* \[&#94;]'LIST'::
    Comma-separated list of samples to include or exclude if prefixed
    with "&#94;".

*-S, --samples-file* [&#94;]'FILE'::
    File of sample names to include or exclude if prefixed with "&#94;".
    One sample per line.
    The command *<<call,bcftools call>>* accepts an optional second
    column indicating ploidy (0, 1 or 2) and can parse also PED files.
    With *<<call,bcftools call>> -C* 'trio', PED file is expected.

*-t, --targets* \[&#94;]'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 "&#94;" to request logical complement. For example, "&#94;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* \[&#94;]'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
----

[[annotate]]
=== 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 "&#94;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,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* \[&#43;]'FORMAT'::
    assign ID on the fly. The format is the same as in the *<<query,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,EXPRESSIONS>>*.

*-o, --output* 'FILE'::
    see *<<common_options,Common Options>>*

*-O, --output-type* 'b'|'u'|'z'|'v'::
    see *<<common_options,Common Options>>*


*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,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* \[&#94;]'LIST'::
    subset of samples to annotate, see also *<<common_options,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
    "&#94;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
----


[[call]]
=== 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
http://github.com/samtools/htslib[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,Common Options>>*

*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,Common Options>>*

*-s, --samples* 'LIST'::
    see *<<common_options,Common Options>>*

*-S, --samples-file* 'FILE'::
    see *<<common_options,Common Options>>*

*-t, --targets* 'LIST'::
    see *<<common_options,Common Options>>*

*-T, --targets-file* 'FILE'::
    see *<<common_options,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,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,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*)


[[concat]]
=== 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,Common Options>>*

*-O, --output-type* 'b'|'u'|'z'|'v'::
    see *<<common_options,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,Common Options>>*. Requires *-a, --allow-overlaps*.

*-R, --regions-file* 'FILE'::
    see *<<common_options,Common Options>>*. Requires *-a, --allow-overlaps*.


[[consensus]]
=== 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,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
----


[[convert]]
=== bcftools convert '[OPTIONS]' 'FILE'

==== VCF input options:

*-e, --exclude* 'EXPRESSION'::
    exclude sites for which 'EXPRESSION' is true. For valid expressions see
    *<<expressions,EXPRESSIONS>>*.

*-i, --include* 'EXPRESSION'::
    include only sites for which 'EXPRESSION' is true. For valid expressions see
    *<<expressions,EXPRESSIONS>>*.

*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-R, --regions-file* 'FILE'::
    see *<<common_options,Common Options>>*

*-s, --samples* 'LIST'::
    see *<<common_options,Common Options>>*

*-S, --samples-file* 'FILE'::
    see *<<common_options,Common Options>>*

*-t, --targets* 'LIST'::
    see *<<common_options,Common Options>>*

*-T, --targets-file* 'FILE'::
    see *<<common_options,Common Options>>*

==== VCF output options:

*-o, --output* 'FILE'::
    see *<<common_options,Common Options>>*

*-O, --output-type* 'b'|'u'|'z'|'v'::
    see *<<common_options,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,Common Options>>*

*-S, --samples-file* 'FILE'::
    file of sample names. See *<<common_options,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
----

[[filter]]
=== bcftools filter '[OPTIONS]' 'FILE'

Apply fixed-threshold filters.

*-e, --exclude* 'EXPRESSION'::
    exclude sites for which 'EXPRESSION' is true. For valid expressions see
    *<<expressions,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,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,Common Options>>*

*-O, --output-type* 'b'|'u'|'z'|'v'::
    see *<<common_options,Common Options>>*

*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,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,Common Options>>*

*-T, --targets-file* 'file'::
    see *<<common_options,Common Options>>*





[[gtcheck]]
=== 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,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,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,Common Options>>*

*-T, --targets-file* 'file'::
    see *<<common_options,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.

//    MD, Maximum Deviation;;
//        The maximum absolute deviation from average score of the sample
//        most dissimilar to the rest.


[[index]]
=== 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&#94;31. TBI (tabix index)
index files, which support chromosome lengths up to 2&#94;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&#94;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.

[[isec]]
=== 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,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,EXPRESSIONS>>*.

*-f, --apply-filters* 'LIST'::
    see *<<common_options,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,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,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,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,Common Options>>*

*-t, --targets* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-T, --targets-file* 'file'::
    see *<<common_options,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
----


[[merge]]
=== 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 *<<norm,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,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,Common Options>>*

*-O, --output-type* 'b'|'u'|'z'|'v'::
    see *<<common_options,Common Options>>*

*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,Common Options>>*



[[norm]]
=== 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,Common Options>>*

*-O, --output-type* 'b'|'u'|'z'|'v'::
    see *<<common_options,Common Options>>*

*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,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,Common Options>>*

*-T, --targets-file* 'FILE'::
    see *<<common_options,Common Options>>*

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


[[plugin]]
=== 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,EXPRESSIONS>>*.

*-i, --include* 'EXPRESSION'::
    include only sites for which 'EXPRESSION' is true. For valid expressions see
    *<<expressions,EXPRESSIONS>>*.

*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,Common Options>>*

*-t, --targets* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-T, --targets-file* 'file'::
    see *<<common_options,Common Options>>*

==== VCF output options:

*-o, --output* 'FILE'::
    see *<<common_options,Common Options>>*

*-O, --output-type* 'b'|'u'|'z'|'v'::
    see *<<common_options,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);
----


[[query]]
=== 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,Common Options>>*

*-e, --exclude* 'EXPRESSION'::
    exclude sites for which 'EXPRESSION' is true. For valid expressions see
    *<<expressions,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,EXPRESSIONS>>*.

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

*-o, --output* 'FILE'::
    see *<<common_options,Common Options>>*

*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,Common Options>>*

*-s, --samples* 'LIST'::
    see *<<common_options,Common Options>>*

*-S, --samples-file* 'FILE'::
    see *<<common_options,Common Options>>*

*-t, --targets* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-T, --targets-file* 'file'::
    see *<<common_options,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


[[reheader]]
=== 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,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.



[[roh]]
=== 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
    be a single file or a file mask, where string "{CHROM}" is replaced with
    chromosome name.

*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,Common Options>>*

*-s, --sample* 'name'::
    the name of sample to analyze

*-t, --targets* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-T, --targets-file* 'file'::
    see *<<common_options,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



[[stats]]
=== 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,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,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,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,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,Common Options>>*

*-s, --samples* 'LIST'::
    see *<<common_options,Common Options>>*

*-S, --samples-file* 'FILE'::
    see *<<common_options,Common Options>>*

*-t, --targets* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-T, --targets-file* 'file'::
    see *<<common_options,Common Options>>*




[[view]]
=== 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,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,Common Options>>*

*-R, --regions-file* 'file'::
    see *<<common_options,Common Options>>*

*-t, --targets* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

*-T, --targets-file* 'file'::
    see *<<common_options,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,Common Options>>*

*-S, --samples-file* 'FILE'::
    see *<<common_options,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,EXPRESSIONS>>*.

*-f, --apply-filters* 'LIST'::
    see *<<common_options,Common Options>>*

*-g, --genotype* [&#94;]['hom'|'het'|'miss']::
    include only sites with one or more homozygous ('hom'), heterozygous
    ('het') or missing ('miss') genotypes. When prefixed with '&#94;', the logic
    is reversed; thus '&#94;het' excludes sites with heterozygous genotypes.

*-i, --include* 'EXPRESSION'::
    include sites for which 'EXPRESSION' is true. For valid expressions see
    *<<expressions,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]]
EXPRESSIONS
-----------

These filtering expressions are accepted by *<<annotate,annotate>>*,
*<<filter,filter>>*, *<<query,query>>* and *<<view,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]]
=== plot-vcfstats ['OPTIONS'] 'file.vchk' [...]
Script for processing output of *<<stats,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 *<<stats,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.

