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


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


SYNOPSIS
--------
*bcftools* [--version|--version-only] [--help] ['COMMAND'] ['OPTIONS']


DESCRIPTION
-----------
BCFtools  is  a set of utilities that manipulate variant calls in the Variant
Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF
will work in all situations. Un-indexed VCF and BCF and streams will
work in most, but not all situations. In general, whenever multiple VCFs are
read simultaneously, they must be indexed and therefore also compressed.

BCFtools is designed to work on a stream. It regards an input file "-" as the
standard input (stdin) and outputs to the standard output (stdout). Several
commands can thus be  combined  with  Unix pipes.


=== VERSION
This manual page was last updated *{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")
- *<<cnv,cnv>>*          ..  Copy Number Variation caller
- *<<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
- *<<csq,csq>>*          ..  haplotype aware consequence caller
- *<<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
- *<<mpileup,mpileup>>*  ..  multi-way pileup producing genotype likelihoods
- *<<norm,norm>>*        ..  normalize indels
- *<<plugin,plugin>>*    ..  run user-defined plugin
- *<<polysomy,polysomy>>*   ..  detect contaminations and whole-chromosome aberrations
- *<<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
- *<<sort,sort>>*        ..  sort VCF/BCF files
- *<<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'.

*--no-version*::
    Do not append version and command line information to the output VCF header.

*-o, --output* 'FILE'::
    When output consists of a single stream, write it to 'FILE' rather than
    to standard output, where it is written by default.

*-O, --output-type* 'b'|'u'|'z'|'v'::
    Output compressed BCF ('b'), uncompressed BCF ('u'), compressed VCF ('z'), uncompressed VCF ('v').
    Use the -Ou option when piping between bcftools subcommands to speed up
    performance by removing unnecessary compression/decompression and
    VCF<-->BCF conversion.

*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    Comma-separated list of regions, see also *-R, --regions-file*. Note
    that *-r* cannot be used in combination with *-R*.

*-R, --regions-file* 'FILE'::
    Regions can be specified either on command line or in a VCF, BED, or
    tab-delimited file (the default).  The columns of the tab-delimited file
    are: CHROM, POS, and, optionally,  POS_TO,  where positions are 1-based
    and inclusive. The columns of the tab-delimited BED file are also
    CHROM, POS and POS_TO (trailing columns are ignored), but coordinates
    are 0-based, half-open.  To indicate that a file be treated as BED rather
    than the 1-based tab-delimited file, the file must have the ".bed" or
    ".bed.gz" suffix (case-insensitive). Uncompressed files are stored in
    memory, while bgzip-compressed and tabix-indexed region files are streamed.
    Note that sequence names must match exactly, "chr20" is not the same as
    "20".  Also note that chromosome ordering in 'FILE' will be respected,
    the VCF will be processed in the order in which chromosomes first appear
    in 'FILE'. However, within chromosomes, the VCF will always be
    processed in ascending genomic coordinate order no matter what order they
    appear in 'FILE'. Note that overlapping regions in 'FILE' can result in
    duplicated out of order positions in the output.
    This option requires indexed VCF/BCF files. Note that *-R* cannot be used
    in combination with *-r*.

*-s, --samples* \[&#94;]'LIST'::
    Comma-separated list of samples to include or exclude if prefixed
    with "&#94;".
    The sample order is updated to reflect that given on the command line.
    Note that in general tags such as INFO/AC, INFO/AN, etc are not updated
    to correspond to the subset samples. *<<view,bcftools view>>* is the
    exception where some tags will be updated (unless the *-I, --no-update*
    option is used; see *<<view,bcftools view>>* documentation). To use updated
    tags for the subset in another command one can pipe from *view* into
    that command. For example:
----
    bcftools view -Ou -s sample1,sample2 file.vcf | bcftools query -f %INFO/AC\t%INFO/AN\n
----

*-S, --samples-file* [&#94;]'FILE'[[samples_file]]::
    File of sample names to include or exclude if prefixed with "&#94;".
    One sample per line. See also the note above for the *-s, --samples*
    option.
    The sample order is updated to reflect that given in the input file.
    The command *<<call,bcftools call>>* accepts an optional second
    column indicating ploidy (0, 1 or 2) or sex (as defined by
    *<<ploidy,--ploidy>>*, for example "F" or "M"), and can parse also PED
    files. If the second column is not present,
    the sex "F" is assumed.
    With *<<call,bcftools call>> -C* 'trio', PED file is expected. File
    formats examples:
----
    sample1    1
    sample2    2
    sample3    2

  or

    sample1    M
    sample2    F
    sample3    F

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

    ignored daughterA fatherA motherA 2
    ignored sonB fatherB motherB 1
----

*-t, --targets* \[&#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.
    Note that the file must be compressed and index.
    Such a file can be easily created from a VCF using:
----
    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
----

*--threads* 'INT'::
    Number of output compression threads to use in addition to main thread.
    Only used when '--output-type' is 'b' or 'z'. Default: 0.


[[annotate]]
=== bcftools annotate '[OPTIONS]' 'FILE'

Add or remove annotations.

*-a, --annotations* 'file'::
    Bgzip-compressed and tabix-indexed file with annotations. The file
    can be VCF, BED, or a tab-delimited file with mandatory columns CHROM, POS
    (or, alternatively, FROM and TO), optional columns REF and ALT, and arbitrary
    number of annotation columns. BED files are expected to have
    the ".bed" or ".bed.gz" suffix (case-insensitive), otherwise a tab-delimited file is assumed.
    Note that in case of tab-delimited file, the coordinates POS, FROM and TO are
    one-based and inclusive.  When REF and ALT are present, only matching VCF
    records will be annotated.
    When multiple ALT alleles are present in the annotation file (given as
    comma-separated list of alleles), at least one must match one of the
    alleles in the corresponding VCF record. Similarly, at least one
    alternate allele from a multi-allelic VCF record must be present in the
    annotation file.
    Note that flag types, such as "INFO/FLAG", can be annotated by including
    a field with the value "1" to set the flag, "0" to remove it, or "." to
    keep existing flags.
    See also *-c, --columns* and *-h, --header-lines*.
----
    # Sample annotation file with columns CHROM, POS, STRING_TAG, NUMERIC_TAG
    1  752566  SomeString      5
    1  798959  SomeOtherString 6
    # etc.
----

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

*-c, --columns* 'list'::
    Comma-separated list of columns or tags to carry over from the annotation file
    (see also *-a, --annotations*). If the annotation file is not a VCF/BCF,
    'list' describes the columns of the annotation file and must include CHROM,
    POS (or, alternatively, FROM and TO), and optionally REF and ALT. Unused
    columns which should be ignored can be indicated by "-".
    +
    If the annotation file is a VCF/BCF, only the edited columns/tags must be present and their
    order does not matter. The columns ID, QUAL, FILTER, INFO and FORMAT
    can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG",
    and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG".
    The imported VCF annotations can be renamed as "DST_TAG:=SRC_TAG" or "FMT/DST_TAG:=FMT/SRC_TAG".
    +
    To carry over all INFO annotations, use "INFO". To add all INFO annotations except
    "TAG", use "&#94;INFO/TAG". By default, existing values are replaced.
    +
    To add annotations without overwriting existing values (that is, to add missing tags or
    add values to existing tags with missing values), use "+TAG" instead of "TAG".
    To append to existing values (rather than replacing or leaving untouched), use "=TAG"
    (instead of "TAG" or "+TAG").
    To replace only existing values without modifying missing annotations, use "-TAG".
    +
    If the annotation file is not a VCF/BCF, all new annotations must be
    defined via *-h, --header-lines*.

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

*-k, --keep-sites*::
    keep sites wich do not pass *-i* and *-e* expressions instead of discarding them

*-m, --mark-sites* [+-]'TAG'::
    annotate sites which are present ("+") or absent ("-") in the *-a* file with a new INFO/TAG flag

*--no-version*::
    see *<<common_options,Common Options>>*

*-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.

*--threads* 'INT'::
    see *<<common_options,Common Options>>*

*-x, --remove* 'list'::
    List of annotations to remove. Use "FILTER" to remove all filters or
    "FILTER/SomeFilter" to remove a specific filter. Similarly, "INFO" can
    be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags
    except GT. To remove all INFO tags except "FOO" and "BAR", use
    "&#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:

*--no-version*::
    see *<<common_options,Common Options>>*

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

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

*--ploidy* 'ASSEMBLY'['?'][[ploidy]]::
    predefined ploidy, use 'list' (or any other unused word) to print a list
    of all predefined assemblies. Append a question mark to print the actual
    definition. See also *--ploidy-file*.

*--ploidy-file* 'FILE'::
    ploidy definition given as a space/tab-delimited list of
    CHROM, FROM, TO, SEX, PLOIDY. The SEX codes are arbitrary and
    correspond to the ones used by *<<samples_file,--samples-file>>*.
    The default ploidy can be given using the starred records (see
    below), unlisted regions have ploidy 2. The default ploidy definition is
----
    X 1 60000 M 1
    X 2699521 154931043 M 1
    Y 1 59373566 M 1
    Y 1 59373566 F 0
    MT 1 16569 M 1
    MT 1 16569 F 1
    *  * *     M 2
    *  * *     F 2
----

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

*--threads* 'INT'::
    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.

*-F, --prior-freqs* 'AN','AC'::
    take advantage of prior knowledge of population allele frequencies. The
    workflow looks like this:
----
    # Extract AN,AC values from an existing VCF, such 1000Genomes
    bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' 1000Genomes.bcf | bgzip -c > AFs.tab.gz

    # If the tags AN,AC are not already present, use the +fill-AN-AC plugin
    bcftools +fill-AN-AC 1000Genomes.bcf | bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' | bgzip -c > AFs.tab.gz
    tabix -s1 -b2 -e2 AFs.tab.gz

    # Create a VCF header description, here we name the tags REF_AN,REF_AC
    cat AFs.hdr
    ##INFO=<ID=REF_AN,Number=1,Type=Integer,Description="Total number of alleles in reference genotypes">
    ##INFO=<ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele">

    # Now before calling, stream the raw mpileup output through `bcftools annotate` to add the frequencies
    bcftools mpileup [...] -Ou | bcftools annotate -a AFs.tab.gz -h AFs.hdr -c CHROM,POS,REF,ALT,REF_AN,REF_AC -Ou | bcftools call -mv -F REF_AN,REF_AC [...]
----

*-g, --gvcf* 'INT'::
    output also gVCF blocks of homozygous REF calls. The parameter 'INT' is the
    minimum per-sample depth required to include a site in the non-variant
    block.

*-i, --insert-missed* 'INT'::
    output also sites missed by mpileup but present in *-T, --targets-file*.

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

*-V, --skip-variants* 'snps'|'indels'::
    skip indel/SNP sites

*-v, --variants-only*::
    output variant sites only

==== Consensus/variant calling options:

*-c, --consensus-caller*::
    the original *samtools*/*bcftools* calling method (conflicts with *-m*)

*-C, --constrain* 'alleles'|'trio'::

        'alleles';;
            call genotypes given alleles. See also *-T, --targets-file*.

        'trio';;
            call genotypes given the father-mother-child constraint. See also
            *-s, --samples* and *-n, --novel-rate*.

*-m, --multiallelic-caller*::
    alternative modelfor multiallelic and rare-variant calling designed to
    overcome known limitations in *-c* calling model (conflicts with *-c*)

*-n, --novel-rate* 'float'[,...]::
    likelihood of novel mutation for constrained *-C* 'trio' calling. The trio
    genotype calling maximizes likelihood of a particular combination of
    genotypes for father, mother and the child
    P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn).
    By providing three values, the mutation rate Pn is set explicitly for SNPs,
    deletions and insertions, respectively.  If two values are given, the first
    is interpreted as the mutation rate of SNPs and the second is used to
    calculate the mutation rate of indels according to their length as
    Pn='float'*exp(-a-b*len), where a=22.8689, b=0.2994 for insertions and
    a=21.9313, b=0.2856 for deletions [pubmed:23975140].  If only one value is
    given, the same mutation rate Pn is used for SNPs and indels.

*-p, --pval-threshold* 'float'::
    with *-c*, accept variant if P(ref|D) < 'float'.

*-P, --prior* 'float'::
    expected substitution rate, or 0 to disable the prior. Only with *-m*.

*-t, --targets* 'file'|'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,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*)


[[cnv]]
=== bcftools cnv '[OPTIONS]' 'FILE'

Copy number variation caller, requires a VCF annotated with the Illumina's
B-allele frequency (BAF) and Log R Ratio intensity (LRR) values. The HMM
considers the following copy number states: CN 2 (normal), 1 (single-copy
loss), 0 (complete loss), 3 (single-copy gain).


==== General Options:

*-c, --control-sample* 'string'::
    optional control sample name. If given, pairwise calling is performed
    and the *-P*  option can be used

*-f, --AF-file* 'file'::
    read allele frequencies from  a tab-delimited file with the columns CHR,POS,REF,ALT,AF

*-o, --output-dir* 'path'::
    output directory

*-p, --plot-threshold* 'float'::
    call *matplotlib* to produce plots for chromosomes with quality at least 'float',
    useful for visual inspection of the calls. With *-p 0*, plots for all chromosomes will be
    generated. If not given, a *matplotlib* script will be created but not called.

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

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

*-s, --query-sample* 'string'::
    query samply name

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

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

==== HMM Options:

*-a, --aberrant* 'float'[,'float']::
    fraction of aberrant cells in query and control. The hallmark of
    duplications and contaminations is the BAF value of heterozygous markers
    which is dependent on the fraction of aberrant cells. Sensitivity to
    smaller fractions of cells can be increased by setting *-a* to a lower value. Note
    however, that this comes at the cost of increased false discovery rate.

*-b, --BAF-weight* 'float'::
    relative contribution from BAF

*-d, --BAF-dev* 'float'[,'float']::
    expected BAF deviation in query and control, i.e. the noise observed
    in the data.

*-e, --err-prob* 'float'::
    uniform error probability

*-l, --LRR-weight* 'float'::
    relative contribution from LRR. With noisy data, this option can have big effect
    on the number of calls produced. In truly random noise (such as in simulated data),
    the value should be set high (1.0), but in the presence of systematic noise
    when LRR are not informative, lower values result in cleaner calls (0.2).

*-L, --LRR-smooth-win* 'int'::
    reduce LRR noise by applying moving average given this window size

*-O, --optimize* 'float'::
    iteratively estimate the fraction of aberrant cells, down to the given fraction.
    Lowering this value from the default 1.0 to say, 0.3, can help discover more
    events but also increases noise

*-P, --same-prob* 'float'::
    the prior probability of the query and the control sample being the same.
    Setting to 0 calls both independently, setting to 1 forces the same copy
    number state in both.

*-x, --xy-prob* 'float'::
    the HMM probability of transition to another copy number state. Increasing this
    values leads to smaller and more frequent calls.



[[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. With the --naive option, the files
are concatenated without being recompressed, which is very fast but dangerous
if the BCF headers differ.


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

*-c, --compact-PS*::
    Do not output PS tag at each site, only at the start of a new phase set block.

*-d, --rm-dups* 'snps'|'indels'|'both'|'all'|'none'::
    Output duplicate records of specified type present in multiple files only once.
    Requires *-a, --allow-overlaps*.

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

*-f, --file-list* 'FILE'::
    Read file names from 'FILE', one file name per line.

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

*--no-version*::
    see *<<common_options,Common Options>>*

*-n, --naive*::
    Concatenate VCF or BCF files without recompression. This is very fast but requires
    that all files are of the same type (all VCF or all BCF) and have the same headers.
    This is because all tags and chromosome names in the BCF body rely on the implicit
    order of the contig and tag definitions in the header. Currently no sanity checks
    are in place. Dangerous, use with caution.

*-o, --output* 'FILE'::
    see *<<common_options,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*.

*--threads* 'INT'::
    see *<<common_options,Common Options>>*


[[consensus]]
=== bcftools consensus '[OPTIONS]' 'FILE'
Create consensus sequence by applying VCF variants to a reference fasta file.
By default, the program will apply all ALT variants to the reference fasta to
obtain the consensus sequence. Using the *--sample* (and, optionally,
*--haplotype*) option will apply genotype (haplotype) calls from FORMAT/GT.
Note that the program does not act as a primitive variant caller and ignores allelic
depth information, such as INFO/AD or FORMAT/AD. For that, consider using the
*setGT* plugin.

*-c, --chain* 'FILE'::
    write a chain file for liftover

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

*-f, --fasta-ref* 'FILE'::
    reference sequence in fasta format

*-H, --haplotype* '1'|'2'|'R'|'A'|'LR'|'LA'|'SR'|'SA'::
    choose which allele from the FORMAT/GT field to use (the codes are case-insensitive):
    
        '1';;
            the first allele

        '2';;
            the second allele

        'R';;
            the REF allele (in heterozygous genotypes)

        'A';;
            the ALT allele (in heterozygous genotypes)

        'LR, LA';;
            the longer allele. If both have the same length, use the REF allele (LR), or the ALT allele  (LA)

        'SR, SA';;
            the shorter allele. If both have the same length, use the REF allele (SR), or the ALT allele  (SA)

    This option requires *-s*, unless exactly one sample is present in the VCF

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

*-I, --iupac-codes*::
    output variants in the form of IUPAC ambiguity codes

*-m, --mask* 'FILE'::
    BED file or TAB file with regions to be replaced with N. See discussion
    of *--regions-file* in *<<common_options,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:

*--no-version*::
    see *<<common_options,Common Options>>*

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

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

*--threads* 'INT'::
    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

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

*--sex* 'FILE'::
    output sex column in the sample file. The FILE format is
----
    MaleSample    M
    FemaleSample  F
----

*--vcf-ids*::
    output VCF IDs in the second column instead of CHROM:POS_REF_ALT


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

*-f, --fasta-ref* 'file'::
    reference sequence in fasta format. Must be indexed with samtools faidx


==== HAP/SAMPLE conversion:
*--hapsample2vcf* 'prefix' or 'hap-file','sample-file'::
    convert from hap/sample format to VCF. The columns of .hap file are
    similar to .gen file above, but there are only two haplotype columns per
    sample. Note that the first column of the .hap file is expected to be in
    the form "CHR:POS_REF_ALT(_END)?", with the _END being optional for
    defining the INFO/END tag when ALT is a symbolic allele, for example:
----
  .hap
  ----
  1:111485207_G_A rsID1 111485207 G A 0 1 0 0
  1:111494194_C_T rsID2 111494194 C T 0 1 0 0
  1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0
----

*--hapsample* 'prefix' or 'hap-file','sample-file'::
    convert from VCF to hap/sample format used by IMPUTE2 and SHAPEIT.
    The columns of .hap file begin with ID,RSID,POS,REF,ALT. In order to
    prevent strand swaps, the program uses IDs of the form
    "CHROM:POS_REF_ALT".

*--haploid2diploid*::
    with *-h* option converts haploid genotypes to homozygous diploid
    genotypes. For example, the program will print '0 0' instead of the
    default '0 -'. This is useful for programs which do not handle haploid
    genotypes correctly.

*--sex* 'FILE'::
    output sex column in the sample file. The FILE format is
----
    MaleSample    M
    FemaleSample  F
----

*--vcf-ids*::
    output VCF IDs instead of "CHROM:POS_REF_ALT" IDs

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

*-h, --haplegendsample* 'prefix' or 'hap-file','legend-file','sample-file'::
    convert from VCF to hap/legend/sample format used by IMPUTE2 and SHAPEIT.
    The columns of .legend file ID,POS,REF,ALT. In order to prevent strand
    swaps, the program uses IDs of the form "CHROM:POS_REF_ALT". The .sample
    file is quite basic at the moment with columns for population, group and
    sex expected to be edited by the user. For example:
----
  .hap
  -----
  0 1 0 0 1 0
  0 1 0 0 0 1

  .legend
  -------
  id position a0 a1
  1:111485207_G_A 111485207 G A
  1:111494194_C_T 111494194 C T

  .sample
  -------
  sample population group sex
  sample1 sample1 sample1 2
  sample2 sample2 sample2 2
----

*--haploid2diploid*::
    with *-h* option converts haploid genotypes to homozygous diploid
    genotypes. For example, the program will print '0 0' instead of the
    default '0 -'. This is useful for programs which do not handle haploid
    genotypes correctly.

*--sex* 'FILE'::
    output sex column in the sample file. The FILE format is
----
    MaleSample    M
    FemaleSample  F
----

*--vcf-ids*::
    output VCF IDs instead of "CHROM:POS_REF_ALT" IDs

==== TSV conversion:
*--tsv2vcf* 'file'::
    convert from TSV (tab-separated values) format (such as generated by
    23andMe) to VCF. The input file fields can be tab- or space- delimited

*-c, --columns* 'list'::
    comma-separated list of fields in the input file. In the current
    version, the fields CHROM, POS, ID, and AA are expected and
    can appear in arbitrary order, columns which should be ignored in the input
    file can be indicated by "-".
    The AA field lists alleles on the forward reference strand,
    for example "CC" or "CT" for diploid genotypes or "C"
    for haploid genotypes (sex chromosomes). Insertions and deletions
    are not supported yet, missing data can be indicated with "--".

*-f, --fasta-ref* 'file'::
    reference sequence in fasta format. Must be indexed with samtools faidx

*-s, --samples* 'LIST'::
    list of sample names. See *<<common_options,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
----


[[csq]]
=== bcftools csq '[OPTIONS]' 'FILE'

Haplotype aware consequence predictor which correctly handles combined
variants such as MNPs split over multiple VCF records, SNPs separated by
an intron (but adjacent in the spliced transcript) or nearby frame-shifting
indels which in combination in fact are not frame-shifting.

The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable
with the *-c* option). The latter is a bitmask of indexes to INFO/BCSQ, with
interleaved haplotypes. See the usage examples below for using the %TBCSQ
converter in *query* for extracting a more human readable form from this
bitmask. The contruction of the bitmask limits the number of consequences
that can be referenced in the FORMAT/BCSQ tags. By default this is 16, but
if more are required, see the *--ncsq* option.

The program requires on input a VCF/BCF file, the reference genome in fasta
format (*--fasta-ref*) and genomic features in the GFF3 format downloadable
from the Ensembl website (*--gff-annot*), and outputs an annotated VCF/BCF
file. Currently, only Ensembl GFF3 files are supported.

By default, the input VCF should be phased. If phase is unknown, or only
partially known, the *--phase* option can be used to indicate how to handle
unphased data. Alternatively, haplotype aware calling can be turned off
with the *--local-csq* option.

If conflicting (overlapping) variants within one haplotype are detected,
a warning will be emitted and predictions will be based on only the first
variant in the analysis.

Symbolic alleles are not supported. They will remain unannotated in the
output VCF and are ignored for the prediction analysis.


*-c, --custom-tag* 'STRING'::
    use this custom tag to store consequences rather than the default BCSQ tag

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

*-f, --fasta-ref* 'FILE'::
    reference sequence in fasta format (required)

*-g, --gff-annot* 'FILE'::
    GFF3 annotation file (required), such as ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens/

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

*-l, --local-csq*::
    switch off haplotype-aware calling, run localized predictions considering
    only one VCF record at a time

*-n, --ncsq* 'INT'::
    maximum number of consequences to consider per site. The INFO/BCSQ column includes
    all consequences, but only the first 'INT' will be referenced by the FORMAT/BCSQ fields.
    The default value is 16 which corresponds to one integer per diploid
    sample. Note that increasing the value leads to increased memory and is rarely necessary.

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

*-O, --output-type* 'b'|'t'|'u'|'z'|'v'::
    see *<<common_options,Common Options>>*. In addition, a custom tab-delimited
    plain text output can be printed ('t').

*-p, --phase* 'a'|'m'|'r'|'R'|'s'::
    how to handle unphased heterozygous genotypes:

        'a';;
            take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)

        'm';;
            merge all GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)

        'r';;
            require phased GTs, throw an error on unphased heterozygous GTs

        'R';;
            create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)

        's';;
            skip unphased heterozygous GTs

*-q, --quiet*::
    suppress warning messages

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

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

*-s, --samples* 'LIST'::
    samples to include or "-" to apply all variants and ignore samples

*-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>>*

*Examples:*
----
    # Basic usage
    bcftools csq -f hs37d5.fa -g Homo_sapiens.GRCh37.82.gff3.gz in.vcf -Ob -o out.bcf

    # Extract the translated haplotype consequences. The following TBCSQ variations
    # are recognised:
    #   %TBCSQ    .. print consequences in all haplotypes in separate columns
    #   %TBCSQ{0} .. print the first haplotype only
    #   %TBCSQ{1} .. print the second haplotype only
    #   %TBCSQ{*} .. print a list of unique consquences present in either haplotype
    bcftools query -f'[%CHROM\t%POS\t%SAMPLE\t%TBCSQ\n]' out.bcf
----

*Examples of BCSQ annotation:*
----
    # Two separate VCF records at positions 2:122106101 and 2:122106102
    # change the same codon. This UV-induced C>T dinucleotide mutation
    # has been annotated fully at the position 2:122106101 with
    #   - consequence type
    #   - gene name
    #   - ensembl transcript ID
    #   - coding strand (+ fwd, - rev)
    #   - amino acid position (in the coding strand orientation)
    #   - list of corresponding VCF variants
    # The annotation at the second position gives the position of the full
    # annotation
    BCSQ=missense|CLASP1|ENST00000545861|-|1174P>1174L|122106101G>A+122106102G>A
    BCSQ=@122106101

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

    # Stop gained variant
    BCSQ=stop_gained|C2orf83|ENST00000264387|-|141W>141*|228476140C>T

    # The consequence type of a variant downstream from a stop are prefixed with *
    BCSQ=*missense|PER3|ENST00000361923|+|1028M>1028T|7890117T>C
----



[[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.

*--no-version*::
    see *<<common_options,Common Options>>*

*-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>>*

*--threads* 'INT'::
    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

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

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

*-g, --genotypes* 'genotypes.vcf.gz'::
    reference genotypes to compare against

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

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

*-p, --plot* 'PREFIX'::
    produce plots

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

*-o, --output-file 'FILE'*::
    output file name. If not set, then the index will be created
    using the input file name plus a '.csi' or '.tbi' extension

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

*--threads* 'INT'::
    see *<<common_options,Common Options>>*

==== Stats options:
*-n, --nrecords*::
    print the number of records based on the CSI or TBI index files

*-s, --stats*::
    Print per contig stats based on the CSI or TBI index files.
    Output format is three tab-delimited columns listing the contig
    name, contig length ('.' if unknown) and number of records for
    the contig. Contigs with zero records are not printed.

[[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'|~'BITMAP'::
    output positions present in this many (=), this many or more (+), this
    many or fewer (-), or the exact same (~) files

*-o, --output* 'FILE'::
    see *<<common_options,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
----

Print a list of records which are present in A and B but not in C and D
----
    bcftools isec -n~1100 -c all A.vcf.gz B.vcf.gz C.vcf.gz D.vcf.gz
----


[[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'

*-0  --missing-to-ref*::
    assume genotypes at missing sites are 0/0

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

*-F, --filter-logic* 'x'|'+'::
    Set the output record to PASS if any of the inputs is PASS ('x'),
    or apply all filters ('+'), which is the default.

*-g, --gvcf* '-'|'FILE'::
    merge gVCF blocks, INFO/END tag is expected. If the reference fasta
    file 'FILE' is not given and the dash ('-') is given, unknown reference
    bases generated at gVCF block splits will be substituted with N's.
    The *--gvcf* option uses the following default INFO rules:
    *-i QS:sum,MinDP:min,I16:sum,IDV:max,IMF:max*.

*-i, --info-rules* '-'|'TAG:METHOD'[,...]::
    Rules for merging INFO fields (scalars or vectors) or '-' to disable the
    default rules. 'METHOD' is one of 'sum', 'avg', 'min', 'max', 'join'.
    Default is 'DP:sum,DP4:sum' if these fields exist in the input files.
    Fields with no specified rule will take the value from the first input file.
    The merged QUAL value is currently set to the maximum. This behaviour is
    not user controllable at the moment.

*-l, --file-list* 'FILE'::
    Read file names from 'FILE', one file name per line.

*-m, --merge* 'snps'|'indels'|'both'|'all'|'none'|'id'::
    The option controls what types of multiallelic records can be created:
----
-m none   ..  no new multiallelics, output multiple records instead
-m snps   ..  allow multiallelic SNP records
-m indels ..  allow multiallelic indel records
-m both   ..  both SNP and indel records can be multiallelic
-m all    ..  SNP records can be merged with indel records
-m id     ..  merge by ID
----

*--no-version*::
    see *<<common_options,Common Options>>*

*-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>>*

*--threads* 'INT'::
    see *<<common_options,Common Options>>*


[[mpileup]]
=== bcftools mpileup ['OPTIONS'] *-f* 'ref.fa' 'in.bam' ['in2.bam' [...]]
Generate VCF or BCF containing genotype likelihoods for one or multiple
alignment (BAM or CRAM) files. This is based on the original
*samtools mpileup* command (with the *-v* or *-g* options) producing
genotype likelihoods in VCF or BCF format, but not the textual pileup
output. The *mpileup* command was transferred to bcftools in order to
avoid errors resulting from use of incompatible versions of samtools
and bcftools when using in the mpileup+bcftools call pipeline.

Individuals are identified from the SM tags in the @RG header lines.  Multiple
individuals can be pooled in one alignment file, also one individual can be
separated into multiple files.  If sample identifiers are absent, each input
file is regarded as one sample.

Note that there are two orthogonal ways to specify locations in the
input file; via *-r* 'region' and *-t* 'positions'.  The
former uses (and requires) an index to do random access while the
latter streams through the file contents filtering out the specified
regions, requiring no index.  The two may be used in conjunction.  For
example a BED file containing locations of genes in chromosome 20
could be specified using *-r 20 -t chr20.bed*, meaning that the
index is used to find chromosome 20 and then it is filtered for the
regions listed in the BED file. Also note that the *-r* option can be much
slower than *-t* with many regions and can require more memory when
multiple regions and many alignment files are processed.


==== Input options

*-6, --illumina1.3+*::
    Assume the quality is in the Illumina 1.3+ encoding.

*-A, --count-orphans*::
    Do not skip anomalous read pairs in variant calling.

*-b, --bam-list* 'FILE'::
    List of input alignment files, one file per line [null]

*-B, --no-BAQ*::
    Disable probabilistic realignment for the computation of base alignment
    quality (BAQ). BAQ is the Phred-scaled probability of a read base being
    misaligned. Applying this option greatly helps to reduce false SNPs caused
    by misalignments.

*-C, --adjust-MQ* 'INT'::
    Coefficient  for  downgrading mapping quality for reads containing
    excessive mismatches. Given a read with a phred-scaled probability q of
    being generated from the mapped posi- tion, the new mapping quality is
    about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if
    enabled, the recommended value for BWA is 50. [0]

*-d, --max-depth* 'INT'::
    At a position, read maximally 'INT' reads per input file. Note that bcftools
    has a minimum value of '8000/n' where 'n' is the number of input files given
    to mpileup.  This means the default is highly likely to be increased. Once
    above the cross-sample minimum of 8000 the -d parameter will have an effect.
    [250]

*-E, --redo-BAQ*::
    Recalculate BAQ on the fly, ignore existing BQ tags

*-f, --fasta-ref* 'FILE'::
    The *faidx*-indexed reference file in the FASTA format. The file can be
    optionally compressed by *bgzip*. Reference is required by default
    unless the *--no-reference* option is set [null]

*--no-reference*::
    Do not require the *--fasta-ref* option.

*-G, --read-groups* [&#94;]'FILE'::
    list of read groups to include or exclude if prefixed with "&#94;".
    One read group per line.  This file can also be used to assign new sample
    names to read groups by giving the new sample name as a second
    white-space-separated field, like this: "read_group_id new_sample_name".
    If the read group name is not unique, also the bam file name can
    be included: "read_group_id file_name sample_name".  If all
    reads from the alignment file should be treated as a single sample, the
    asterisk symbol can be used: "* file_name sample_name". Alignments without
    a read group ID can be matched with "?". *NOTE:* The meaning of *bcftools mpileup -G*
    is the opposite of *samtools mpileup -G*.
----
    RG_ID_1
    RG_ID_2  SAMPLE_A
    RG_ID_3  SAMPLE_A
    RG_ID_4  SAMPLE_B
    RG_ID_5  FILE_1.bam  SAMPLE_A
    RG_ID_6  FILE_2.bam  SAMPLE_A
    *        FILE_3.bam  SAMPLE_C
    ?        FILE_3.bam  SAMPLE_D
----

*-q, -min-MQ* 'INT'::
    Minimum mapping quality for an alignment to be used [0]

*-Q, --min-BQ* 'INT'::
    Minimum base quality for a base to be considered [13]

*-r, --regions* 'CHR'|'CHR:POS'|'CHR:FROM-TO'|'CHR:FROM-'[,...]::
    Only generate mpileup output in given regions. Requires the alignment files
    to be indexed.  If used in conjunction with -l then considers the intersection;
    see *<<common_options,Common Options>>*

*-R, --regions-file* 'FILE'::
    As for *-r, --regions*, but regions read from FILE;
    see *<<common_options,Common Options>>*

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

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

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

*-s, --samples* [&#94;]'LIST'::
    list of sample names. See *<<common_options,Common Options>>*

*-S, --samples-file* [&#94;]'FILE'::
    file of sample names to include or exclude if prefixed with "&#94;".
    One sample per line. This file can also be used to rename samples by giving
    the new sample name as a second white-space-separated column, like this:
    "old_name new_name".  If a sample name contains spaces, the spaces can be
    escaped using the backslash character, for example "Not\ a\ good\ sample\
    name".

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

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

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


==== Output options

*-a, --annotate* 'LIST'::
    Comma-separated list of FORMAT and INFO tags to output. (case-insensitive,
    the "FORMAT/" prefix is optional, and use "?" to list available annotations
    on the command line) [null]:

    *FORMAT/AD* .. Allelic depth (Number=R,Type=Integer)
    *FORMAT/ADF* .. Allelic depths on the forward strand (Number=R,Type=Integer)
    *FORMAT/ADR* .. Allelic depths on the reverse strand (Number=R,Type=Integer)
    *FORMAT/DP* .. Number of high-quality bases (Number=1,Type=Integer)
    *FORMAT/SP* .. Phred-scaled strand bias P-value (Number=1,Type=Integer)

    *INFO/AD* .. Total allelic depth (Number=R,Type=Integer)
    *INFO/ADF* .. Total allelic depths on the forward strand (Number=R,Type=Integer)
    *INFO/ADR* .. Total allelic depths on the reverse strand (Number=R,Type=Integer)

    *FORMAT/DV* .. Deprecated in favor of FORMAT/AD;
            Number of high-quality non-reference bases, (Number=1,Type=Integer)
    *FORMAT/DP4* .. Deprecated in favor of FORMAT/ADF and FORMAT/ADR;
            Number of high-quality ref-forward, ref-reverse,
            alt-forward and alt-reverse bases (Number=4,Type=Integer)
    *FORMAT/DPR* .. Deprecated in favor of FORMAT/AD;
            Number of high-quality bases for each observed allele (Number=R,Type=Integer)
    *INFO/DPR* .. Deprecated in favor of INFO/AD;
            Number of high-quality bases for each observed allele (Number=R,Type=Integer)

*-g, --gvcf* 'INT'[,...]::
    output gVCF blocks of homozygous REF calls, with depth (DP) ranges
    specified by the list of integers. For example, passing '5,15' will
    group sites into two types of gVCF blocks, the first with minimum
    per-sample DP from the interval [5,15) and the latter with minimum
    depth 15 or more. In this example, sites with minimum per-sample
    depth less than 5 will be printed as separate records, outside of
    gVCF blocks.

*--no-version*::
    see *<<common_options,Common Options>>*

*-o, --output* 'FILE'::
    Write output to 'FILE', rather than the default of standard output.
    (The same short option is used for both *--open-prob* and *--output*.  If *-o*'s
    argument contains any non-digit characters other than a leading + or -
    sign,  it  is  interpreted  as *--output*.  Usually the filename extension
    will take care of this, but to write to an entirely numeric filename use *-o
    ./123* or *--output 123*.)

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

*--threads* 'INT'::
    see *<<common_options,Common Options>>*

==== Options for SNP/INDEL genotype likelihood computation

*-e, --ext-prob* 'INT'::
    Phred-scaled gap extension sequencing error probability. Reducing 'INT'
    leads to longer indels [20]

*-F, --gap-frac* 'FLOAT'::
    Minimum fraction of gapped reads [0.002]

*-h, --tandem-qual* 'INT'::
    Coefficient for modeling homopolymer errors. Given an 'l'-long homopolymer
    run, the sequencing error of an indel of size s is modeled as 'INT'*s/l [100]

*-I, --skip-indels*::
    Do not perform INDEL calling

*-L, --max-idepth* 'INT'::
    Skip INDEL calling if the average per-sample depth is above 'INT' [250]

*-m, --min-ireads* 'INT'::
    Minimum number gapped reads for indel candidates 'INT' [1]

*-o, --open-prob* 'INT'::
    Phred-scaled gap open sequencing error probability. Reducing 'INT' leads
    to more indel calls. (The same short option is used for both *--open-prob*
    and *--output*.  When -o's argument contains only an optional + or - sign
    followed by the digits 0 to 9, it is interpreted  as *--open-prob*.) [40]

*-p, --per-sample-mF*::
    Apply *-m* and *-F* thresholds per sample to increase sensitivity of calling.
    By default both options are applied to reads pooled from all samples.

*-P, --platforms* 'STR'::
    Comma-delimited  list  of  platforms (determined by *@RG-PL*) from which
    indel candidates are obtained. It is recommended to collect indel
    candidates from sequencing technologies that have low indel error rate
    such as ILLUMINA [all]

==== Examples:

Call SNPs and short INDELs, then mark low quality sites and sites with the read
depth exceeding a limit. (The read depth should be adjusted to about twice the
average read depth as higher read depths usually indicate problematic regions
which are often enriched for artefacts.) One may consider to add *-C50* to
mpileup if mapping quality is overestimated  for reads containing  excessive
mismatches.  Applying this option usually helps for BWA-backtrack alignments,
but may not other aligners.
----
    bcftools mpileup -Ou -f ref.fa aln.bam | \
    bcftools call -Ou -mv | \
    bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > var.flt.vcf
----


[[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. Left-alignment and normalization will only be applied if
the *<<fasta_ref,--fasta-ref>>* option is supplied.

*-c, --check-ref* 'e'|'w'|'x'|'s'::
    what to do when incorrect or missing REF allele is encountered:
    exit ('e'), warn ('w'), exclude ('x'), or set/fix ('s') bad sites.
    The 'w' option can be combined with 'x' and 's'. Note that 's'
    can swap alleles and will update genotypes (GT) and AC counts,
    but will not attempt to fix PL or other fields.

*-d, --rm-dup* 'snps'|'indels'|'both'|'any'::
    If a record is present multiple times, output only the first instance,
    see *--collapse* in *<<common_options,Common Options>>*.

*-D, --remove-duplicates*::
    If a record is present in multiple files, output only the first instance.
    Alias for *-d none*.  Requires *-a, --allow-overlaps*.

*-f, --fasta-ref* 'FILE'[[fasta_ref]]::
    reference sequence. Supplying this option will turn on left-alignment
    and normalization, however, see also the *<<do_not_normalize,--do-not-normalize>>*
    option below.

*-m, --multiallelics* *-*|*+*['snps'|'indels'|'both'|'any']::
    split multiallelic sites into biallelic records (*-*) or join
    biallelic sites into multiallelic records (*+*). An optional type string
    can follow which controls variant types which should be split or merged
    together: If only SNP records should be split or merged, specify 'snps'; if
    both SNPs and indels should be merged separately into two records, specify
    'both'; if SNPs and indels should be merged into a single record, specify
    'any'.

*--no-version*::
    see *<<common_options,Common Options>>*

*-N, --do-not-normalize*[[do_not_normalize]]::
    the '-c s' option can be used to fix or set the REF allele from the
    reference '-f'. The '-N' option will not turn on indel normalisation
    as the '-f' option normally implies

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

*--threads* 'INT'::
    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'|+'NAME'] '[OPTIONS]' 'FILE' -- '[PLUGIN OPTIONS]'

A common framework for various utilities. The plugins can be used
the same way as normal commands only their name is prefixed with "+".
Most plugins accept two types of parameters: general options shared by all
plugins followed by a separator, and a list of plugin-specific options.  There
are some exceptions to this rule, some plugins do not accept the common
options and implement their own parameters. Therefore please pay attention to
the usage examples that each plugin comes with.



==== VCF input options:

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

*--no-version*::
    see *<<common_options,Common Options>>*

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

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

*--threads* 'INT'::
    see *<<common_options,Common Options>>*

==== Plugin options:

*-h, --help*::
    list plugin's options

*-l, --list-plugins*::
    List all available plugins.
+
By default, appropriate system directories are searched for installed plugins.
    You can override this by setting the BCFTOOLS_PLUGINS environment variable
    to a colon-separated list of directories to search.
    If BCFTOOLS_PLUGINS begins with a colon, ends with a colon, or contains
    adjacent colons, the system directories are also searched at that position
    in the list of directories.

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

*-V, --version*::
    print version string and exit

==== List of plugins coming with the distribution:

*GTisec*::
    count genotype intersections across all possible sample subsets in a vcf file

*GTsubset*::
    output only sites where the requested samples all exclusively share a genotype

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

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

*check-ploidy*::
    check if ploidy of samples is consistent for all sites

*check-sparsity*::
    print samples without genotypes in a region or chromosome

*color-chrs*::
    color shared chromosomal segments, requires trio VCF with phased GTs

*counts*::
    a minimal plugin which counts number of SNPs, Indels, and total number of sites.

*dosage*::
    print genotype dosage. By default the plugin searches for PL, GL and GT, in
    that order.

*fill-AN-AC*::
    fill INFO fields AN and AC.

*fill-from-fasta*::
    fill INFO or REF field based on values in a fasta file

*fill-tags*::
    set INFO tags AF, AC, AC_Hemi, AC_Hom, AC_Het, AN, HWE, MAF, NS

*fix-ploidy*::
    sets correct ploidy

*fixref*::
    determine and fix strand orientation

*frameshifts*::
    annotate frameshift indels

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

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

*isecGT*::
    compare two files and set non-identical genotypes to missing

*mendelian*::
    count Mendelian consistent / inconsistent genotypes.

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

*prune*::
    prune sites by missingness or linkage disequilibrium

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

*tag2tag*::
    convert between similar tags, such as GL and GP

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


==== Examples:

----
# List options common to all plugins
bcftools plugin

# List available plugins
bcftools plugin -l

# Run a plugin
bcftools plugin counts in.vcf

# Run a plugin using the abbreviated "+" notation
bcftools +counts in.vcf

# The input VCF can be streamed just like in other commands
cat in.vcf | bcftools +counts

# Print usage information of plugin "dosage"
bcftools +dosage -h

# Replace missing genotypes with 0/0
bcftools +missing2ref in.vcf

# Replace missing genotypes with 0|0
bcftools +missing2ref in.vcf -- -p
----

==== Plugins troubleshooting:

Things to check if your plugin does not show up in the *bcftools plugin -l* output:

- Run with the *-v* option for verbose output: *bcftools plugin -lv*
- Does the environment variable BCFTOOLS_PLUGINS include the correct path?


==== Plugins API:

----
// Short description used by 'bcftools plugin -l'
const char *about(void);

// Longer description used by 'bcftools +name -h'
const char *usage(void);

// Called once at startup, allows initialization of local variables.
// Return 1 to suppress normal VCF/BCF header output, -1 on critical
// errors, 0 otherwise.
int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr);

// Called for each VCF record, return NULL to suppress the output
bcf1_t *process(bcf1_t *rec);

// Called after all lines have been processed to clean up
void destroy(void);
----



[[polysomy]]
=== bcftools polysomy ['OPTIONS'] 'file.vcf.gz'
Detect number of chromosomal copies in VCFs annotates with the Illumina's
B-allele frequency (BAF) values. Note that this command is not compiled
in by default, see the section *Optional Compilation with GSL* in the INSTALL
file for help.

==== General options:

*-o, --output-dir* 'path'::
    output directory

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

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

*-s, --sample* 'string'::
    sample name

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

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

*-v, --verbose*::
    verbose debugging output which gives hints about the thresholds and decisions made
    by the program. Note that the exact output can change between versions.

==== Algorithm options:

*-b, --peak-size* 'float'::
    the minimum peak size considered as a good match can be from the interval [0,1]
    where larger is stricter

*-c, --cn-penalty* 'float'::
    a penalty for increasing copy number state. How this works: multiple peaks
    are always a better fit than a single peak, therefore the program prefers
    a single peak (normal copy number) unless the absolute deviation of the
    multiple peaks fit is significantly smaller. Here the meaning of
    "significant" is given by the 'float' from the interval [0,1] where
    larger is stricter.

*-f, --fit-th* 'float'::
    threshold for goodness of fit (normalized absolute deviation), smaller is stricter

*-i, --include-aa*::
    include also the AA peak in CN2 and CN3 evaluation. This usually requires increasing *-f*.

*-m, --min-fraction* 'float'::
    minimum distinguishable fraction of aberrant cells. The experience shows that trustworthy
    are estimates of 20% and more.

*-p, --peak-symmetry* 'float'::
    a heuristics to filter failed fits where the expected peak symmetry is violated.
    The 'float' is from the interval [0,1] and larger is stricter


[[query]]
=== bcftools query ['OPTIONS'] 'file.vcf.gz' ['file.vcf.gz' [...]]
Extracts fields from VCF or BCF files and outputs them in user-defined format.

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

*-u, --allow-undef-tags*::
    do not throw an error if there are undefined tags in the format string,
    print "." instead

*-v, --vcf-list* 'FILE'::
    process multiple VCFs listed in the file

==== Format:

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

    Everything else is printed verbatim.

==== Examples:

    # Print chromosome, position, ref allele and the first alternate allele
    bcftools query -f '%CHROM  %POS  %REF  %ALT{0}\n' file.vcf.gz

    # Similar to above, but use tabs instead of spaces, add sample name and genotype
    bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz

    # Print FORMAT/GT fields followed by FORMAT/GT fields
    bcftools query -f 'GQ:[ %GQ] \t GT:[ %GT]\n' file.vcf

    # Make a BED file: chr, pos (0-based), end pos (1-based), id
    bcftools query -f'%CHROM\t%POS0\t%END\t%ID\n' file.bcf

    # Print only samples with alternate (non-reference) genotypes
    bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf

    # Print all samples at sites with at least one alternate genotype
    bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]'

[[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 a separate line. If a sample name contains spaces, the
    spaces can be escaped using the backslash character, for example
    "Not\ a\ good\ sample\ name".


[[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

  ci  = P_i(C)  .. probability of cross-over at site i, from genetic map
  AZi = P_i(AZ) .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
  HWi = P_i(HW)

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

--------------------------------------

==== General Options:

*--AF-dflt* 'FLOAT'::
    in case allele frequency is not known, use the 'FLOAT'. By default, sites where
    allele frequency cannot be determined, or is 0, are skipped.

*--AF-tag* 'TAG'::
    use the specified INFO tag 'TAG' as an allele frequency estimate
    instead of the default AC and AN tags. Sites which do not have 'TAG'
    will be skipped.

*--AF-file* 'FILE'::
    Read allele frequencies from a tab-delimited file containing
    the columns: CHROM\tPOS\tREF,ALT\tAF. The file can be compressed with
    *bgzip* and indexed with tabix -s1 -b2 -e2.  Sites which are not present in
    the 'FILE' or have different reference or alternate allele will be skipped.
    Note that such a file can be easily created from a VCF using:
----
    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\t%INFO/TAG\n' file.vcf | bgzip -c > freqs.tab.gz
----

*-b, --buffer-size* 'INT'[,'INT']::
    when the entire many-sample file cannot fit into memory, a sliding
    buffer approach can be used. The first value is the number of sites
    to keep in memory. If negative, it is interpreted as the maximum
    memory to use, in MB. The second, optional, value sets the number
    of overlapping sites. The default overlap is set to roughly 1% of
    the buffer size.

*-e, --estimate-AF* ['TAG',]'FILE'::
    estimate the allele frequency by recalculating INFO/AC and INFO/AN on
    the fly, using the specified 'TAG' which can be either FORMAT/GT ("GT")
    or FORMAT/PL ("PL"). If 'TAG' is not given, "GT" is assumed.  Either all
    samples ("-") or samples listed in 'FILE' will be included. For example,
    use "PL,-" to estimate AF from FORMAT/PL of all samples.
    If neither *-e* nor the other *--AF-...* options are given, the allele frequency is
    estimated from AC and AN counts which are already present in the INFO field.

*-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.

*-M, --rec-rate* 'FLOAT'::
    constant recombination rate per bp. In combination with *--genetic-map*,
    the *--rec-rate* parameter is interpreted differently, as 'FLOAT'-fold increase of 
    transition probabilities, which allows the model to become more sensitive
    yet still account for recombination hotspots. Note that also the range
    of the values is therefore different in both cases: normally the
    parameter will be in the range (1e-3,1e-9) but with *--genetic-map* 
    it will be in the range (10,1000).

*-o, --output* 'FILE'::
    Write output to the 'FILE', by default the output is printed on stdout

*-O, --output-type* 's'|'r'['z']::
    Generate per-site output ('s') or per-region output ('r'). By default
    both types are printed and the output is uncompressed. Add 'z' for
    a compressed output.

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

==== HMM Options:

*-a, --hw-to-az* 'FLOAT'::
    P(AZ|HW) transition probability from AZ (autozygous) to HW (Hardy-Weinberg) state

*-H, --az-to-hw* 'FLOAT'::
    P(HW|AZ) transition probability from HW to AZ state

*-V, --viterbi-training* 'FLOAT'::
    estimate HMM parameters using Baum-Welch algorithm, using the convergence threshold
    'FLOAT', e.g. 1e-10 (experimental)


[[sort]]
=== bcftools sort ['OPTIONS'] file.bcf

*-m, --max-mem* 'FLOAT'['kMG']::
    Maximum memory to use. Approximate, affects the number of temporary files written
    to the disk. Note that if the command fails at this step because of too many open files,
    your system limit on the number of open files ("ulimit") may need to be increased.

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

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

*-T, --temp-dir* 'DIR'::
    Use this directory to store temporary files



[[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.
When one VCF file is specified on the command line, then stats by non-reference allele
frequency, depth distribution, stats by quality and per-sample counts, singleton stats,
etc. are printed.
When two VCF files are given, then stats such as concordance (Genotype concordance by
non-reference allele frequency, Genotype concordance by sample, Non-Reference Discordance)
and correlation are also printed. Per-site discordance (PSD) is also printed in *--verbose* mode.

*--af-bins* 'LIST'|'FILE'::
    comma separated list of allele frequency bins (e.g. 0.1,0.5,1)
    or a file listing the allele frequency bins one per line (e.g. 0.1\n0.5\n1)

*--af-tag* 'TAG'::
    allele frequency INFO tag to use for binning. By default the allele frequency is
    estimated from AC/AN, if available, or directly from the genotypes (GT) if not.

*-1, --1st-allele-only*::
    consider only the 1st alternate allele at multiallelic sites

*-c, --collapse* 'snps'|'indels'|'both'|'all'|'some'|'none'::
    see *<<common_options,Common Options>>*

*-d, --depth* 'INT','INT','INT'::
    ranges of depth distribution: min, max, and size of the bin

*--debug*::
    produce verbose per-site and per-sample output

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

*-E, --exons* 'file.gz'::
    tab-delimited file with exons for indel frameshifts statistics. The columns
    of the file are CHR, FROM, TO, with 1-based, inclusive, positions. The file
    is BGZF-compressed and indexed with tabix
----
    tabix -s1 -b2 -e3 file.gz
----

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

*-F, --fasta-ref* 'ref.fa'::
    faidx indexed reference sequence file to determine INDEL context

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

*-I, --split-by-ID*::
    collect stats separately for sites which have the ID column set ("known
    sites") or which do not have the ID column set ("novel sites").

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

*-u, --user-tstv* '<TAG[:min:max:n]>'::
    collect Ts/Tv stats for any tag using the given binning [0:1:100]

*-v, --verbose*::
    produce verbose per-site and per-sample output


[[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.

*--no-version*::
    see *<<common_options,Common Options>>*

*-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>>*

*--threads* 'INT'::
    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

*--force-samples*::
    only warn about unknown subset samples

*-I, --no-update*::
    do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)

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

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


==== Filter options:
Note that filter options below dealing with counting the number of alleles
will, for speed, first check for the values of AC and AN in the INFO column to
avoid parsing all the genotype (FORMAT/GT) fields in the VCF. This means
that a filter like '--min-af 0.1' will be based `AC/AN' where AC and AN come
from either INFO/AC and INFO/AN if available or FORMAT/GT if not. It will not
filter on another field like INFO/AF. The '--include' and '--exclude' filter
expressions should instead be used to explicitly filter based on fields in
the INFO column, e.g. '--exclude AF<0.1'.

*-c, --min-ac* 'INT'[':nref'|':alt1'|':minor'|':major'|:'nonmajor']::
    minimum allele count (INFO/AC) of sites to be printed.
    Specifying the type of allele is optional and can be set to
    non-reference ('nref', the default), 1st alternate  ('alt1'), the least
    frequent ('minor'), the most frequent ('major') or sum of all but the
    most frequent ('nonmajor') alleles.

*-C, --max-ac* 'INT'[':nref'|':alt1'|':minor'|:'major'|:'nonmajor']::
    maximum allele count (INFO/AC) of sites to be printed.
    Specifying the type of allele is optional and can be set to
    non-reference ('nref', the default), 1st alternate  ('alt1'), the least
    frequent ('minor'), the most frequent ('major') or sum of all but the
    most frequent ('nonmajor') alleles.

*-e, --exclude* 'EXPRESSION'::
    exclude sites for which 'EXPRESSION' is true. For valid expressions see
    *<<expressions,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. Site is selected if
    any of the ALT alleles is of the type requested. Types are determined
    by comparing the REF and ALT alleles in the VCF record not INFO tags
    like INFO/INDEL or INFO/VT. Use *--include* to select based on INFO
    tags.

*-V, --exclude-types* 'snps'|'indels'|'mnps'|'ref'|'bnd'|'other'::
    comma-separated list of variant types to exclude. Site is excluded if
    any of the ALT alleles is of the type requested. Types are determined
    by comparing the REF and ALT alleles in the VCF record not INFO tags
    like INFO/INDEL or INFO/VT. Use *--exclude* to exclude based on INFO tags.

*-x, --private*::
    print sites where only the subset samples carry an non-reference allele.
    Requires *--samples* or *--samples-file*.

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

[[help]]
=== bcftools help ['COMMAND'] | bcftools --help ['COMMAND']
Display  a  brief usage message listing the bcftools commands available.
If the name of a command is also given, e.g., bcftools help view, the detailed
usage message for that particular command is displayed.

[[version]]
=== bcftools ['--version'|'-v']
Display the version numbers and copyright information for bcftools and the
important libraries used by bcftools.

[[version-only]]
=== bcftools ['--version-only']
Display the full bcftools version number in a machine-readable format.


[[expressions]]
EXPRESSIONS
-----------

These filtering expressions are accepted by most of the commands.

.Valid expressions may contain:

* numerical constants, string constants, file names

        1, 1.0, 1e-4
        "String"
        @file_name


* arithmetic operators

        +,*,-,/

* comparison operators

        == (same as =), >, >=, <=, <, !=

* regex operators "\~" and its negation "!~". The expressions are case sensitive unless "/i" is added.

        INFO/HAYSTACK ~ "needle"
        INFO/HAYSTACK ~ "NEEDless/i"

* parentheses

        (, )

* logical operators

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

* INFO tags, FORMAT tags, column names

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

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

        FlagA=1 && FlagB=0

* "." to test missing values

        DP=".", DP!=".", ALT="."

* missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".")
using these expressions

        GT~"\.", GT!~"\."

* missing genotypes can be matched including the phase and ploidy (".|.", "./.", ".")
using these expressions

        GT=".|.", GT="./.", GT="."

* sample genotype: reference (haploid or diploid), alternate (hom or het,
haploid or diploid), missing genotype, homozygous, heterozygous, haploid,
ref-ref hom, alt-alt hom, ref-alt het, alt-alt het, haploid ref, haploid alt
(case-insensitive)

        GT="ref"
        GT="alt"
        GT="mis"
        GT="hom"
        GT="het"
        GT="hap"
        GT="RR"
        GT="AA"
        GT="RA" or GT="AR"
        GT="Aa" or GT="aA"
        GT="R"
        GT="A"

* TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,bnd,other). Use the regex
operator "\~" to require at least one allele of the given type or the equal sign "="
to require that all alleles are of the given type. Compare

        TYPE="snp"
        TYPE~"snp"
        TYPE!="snp"
        TYPE!~"snp"

* array subscripts (0-based), "*" for any field, "-" to indicate a range. Note that
for querying FORMAT vectors, the colon ":" can be used to select a sample and a subfield

        (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
        DP4[*] == 0
        CSQ[*] ~ "missense_variant.*deleterious"
        FORMAT/DP[0]   > 30         .. DP of the first sample bigger than 30
        FORMAT/DP[1-3] > 10         .. samples 2-4
        FORMAT/DP[1-]  < 7          .. all samples but the first
        FORMAT/DP[0,2-4] > 20       .. samples 1, 3-5
        FORMAT/AD[0:1]              .. first sample, second AD field
        FORMAT/AD[0:*], AD[0:] or AD[0] .. first sample, any AD field
        FORMAT/AD[*:1] or AD[:1]        .. any sample, second AD field

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

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

* variables calculated on the fly if not present: number of alternate alleles;
number of samples; count of alternate alleles; minor allele count (similar to
AC but is always smaller than 0.5); frequency of alternate alleles (AF=AC/AN);
frequency of minor alleles (MAF=MAC/AN); number of alleles in called genotypes;
number of samples with missing genotype; fraction of samples with missing genotype

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


.Notes:

* String comparisons and regular expressions are case-insensitive
* Variables and function names are case-insensitive, but not tag names. For example,
"qual" can be used instead of "QUAL", "strlen()" instead of "STRLEN()" , but
not "dp" instead of "DP".
* When querying multiple subfields, all subfields are tested and the OR logic is
used on the result. For example, when querying "TAG=1,2,3,4", it will be evaluated as follows:

    -i 'TAG[*]=1'   .. true, the record will be printed
    -i 'TAG[*]!=1'  .. true
    -e 'TAG[*]=1'   .. false, the record will be discarded
    -e 'TAG[*]!=1'  .. false
    -i 'TAG[0]=1'   .. true
    -i 'TAG[0]!=1'  .. false
    -e 'TAG[0]=1'   .. false
    -e 'TAG[0]!=1'  .. true


*Examples:*

--
    MIN(DV)>5

    MIN(DV/DP)>0.3

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

    FMT/DP>10  & FMT/GQ>10 .. both conditions must be satisfied within one sample

    FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples

    QUAL>10 |  FMT/GQ>10   .. true for sites with QUAL>10 or a sample with GQ>10, but selects only samples with GQ>10

    QUAL>10 || FMT/GQ>10   .. true for sites with QUAL>10 or a sample with GQ>10, plus selects all samples at such sites

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

    COUNT(GT="hom")=0

    MIN(DP)>35 && AVG(GQ)>50

    ID=@file       .. selects lines with ID present in the file

    ID!=@~/file    .. skip lines with ID present in the ~/file

    MAF[0]<0.05    .. select rare variants at 5% cutoff

    POS>=100   .. restrict your range query, e.g. 20:100-200 to strictly sites with POS in that range.

--

*Shell expansion:*

Note that expressions must often be quoted because some characters
have special meaning in the shell.
An example of expression enclosed in single quotes which cause
that the whole expression is passed to the program as intended:

--
    bcftools view -i '%ID!="." & MAF[0]<0.01'
--

Please refer to the documentation of your shell for details.


SCRIPTS AND OPTIONS
-------------------

[[plot-vcfstats]]
=== 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* 'DIR'::
    The output directory. This directory will be created if it does not exist.

*-P, --no-PDF*::
    Skip the PDF creation step.

*-r, --rasterize*::
    Rasterize PDF images for faster rendering.

*-s, --sample-names*::
    Use sample names for xticks rather than numeric IDs.

*-t, --title* 'STRING'::
    Identify files by these titles in plots. The option can be given multiple
    times, for each ID in the *<<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.

