bcftools.txt

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


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


SYNOPSIS
--------
*bcftools* ['COMMAND'] ['OPTIONS']


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

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.


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.

- *index*                ..  index VCF/BCF
- *<<annotate,annotate>>*   .. edit VCF files, add or remove annotations, apply user plugins
- *<<call,call>>*        ..  SNP/indel calling (former "view")
- *<<filter,filter>>*    ..  filter VCF/BCF files using fixed thresholds
- *<<gtcheck,gtcheck>>*  ..  check sample concordance, detect sample swaps and contamination
- *<<isec,isec>>*        ..  intersections of VCF/BCF files
- *<<merge,merge>>*      ..  merge VCF/BCF files to create multi-sample file
- *<<norm,norm>>*        ..  normalize indels
- *<<query,query>>*      ..  transform VCF/BCF into user-defined formats
- *<<roh,roh>>*          ..  identify runs of homo/auto-zygosity
- *<<stats,stats>>*      ..  produce VCF/BCF stats (former vcfcheck)
- *<<view,view>>*        ..  subset, filter and convert VCF and BCF files
- *<<plot-vcfstats,plot-vcfstats>>*  .. plots the output of *<<stats,stats>>*


OPTIONS
-------

[[common_options]]
=== Common Options

'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'::
    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'"

*-f, --apply-filters* 'LIST'::
    Skip sites where FILTER column does not contain any of the strings listed
    in 'LIST'. For example, to include only sites which have no filters set,
    use *-f* '.,PASS'.

*-O, --output-type* 'b'|'u'|'z'|'v'::
    Output compressed BCF ('b'), uncompressed BCF ('u'), compressed VCF ('z'), uncompressed VCF ('v').

*-r, --regions* 'file'|'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    Regions can be specified either on command line or in a VCF, BED, or
    tab-delimited file (the default).  The columns of the tab-delimited file
    are: CHROM, POS, and,  optionally,  POS_TO,  where positions are 1-based
    and inclusive.  Uncompressed files are stored in memory, while
    bgzip-compressed and tabix-indexed region files are streamed.  Note that
    sequence names must match exactly, "chr20" is not the same as "20".  This
    option requires indexed VCF/BCF files.

*-s, --samples* 'LIST'|':FILE'::
    Comma-separated list of samples to include or, when prefixed with colon
    ':', read sample names from 'FILE' with one sample per line.
    The command *<<call,bcftools call>>* accepts an optional second
    column indicating ploidy (0, 1 or 2) and can parse also PED files.
    With *<<call,bcftools call>> -C* 'trio', PED file is expected.

*-t, --targets* 'file'|'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    Same 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.  Another difference
    between the two is that *-r* checks both start and end positions of indels,
    whereas *-t* checks start positions only.  With the call *-C* 'alleles' command,
    third column of the targets file must be comma-separated list of alleles,
    starting with the reference allele. Such a file can be easily created from
    a VCF with:
----
    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf
----

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

This command allows to add or remove annotations and apply user-written plugins.

*-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, TO), optional columns REF and ALT, and arbitrary
    number of annotation columns. 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.
    See also *-c, --columns* and *-h, --header-lines*.

*-c, --columns* 'list'::
    Comma-separated list of columns present in the annotation file and defined
    in the header file (see also *-a, --annotations* and *-h, --header-lines*).
    INFO tags can be written both as INFO/TAG or simply TAG. Unused columns can
    be indicated by '-'.  For example:
----
    CHROM,FROM,TO,REF,ALT,-,INFO/TAG
----

*-h, --header-lines* 'file'::
    Header lines to appended to the VCF header.

*-l, --list-plugins*::
    List of available plugins. The BCFTOOLS_PLUGINS environment variable tells
    the program which directories to search:

        missing2ref;; Sets missing genotypes ("./.") to ref allele ("0/0").

        fill-AN-AC;;  Fills INFO fields AN and AC.

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

*-p, --plugins* 'name'[,...]::
    Comma-separated list of plugins to run. The BCFTOOLS_PLUGINS environment
    variable tells the program which directories to search.
    See the examples in plugins/\*.c coming with this distribution for further
    details and examples. See *-l, --list-plugins* to get a list of installed
    plugins.

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

*-R, --remove* 'list':: 
    List of annotations to remove. Use 'FILTER' to remove all filters or
    'FILTER/SomeFilter' to remove a specific filter. More examples:
----
    ID,INFO/DP,FORMAT/DP
----



[[call]]
=== bcftools call '[OPTIONS]' 'FILE'

This command replaces the former *bcftools view* caller. Some of the original
functionality has been temporarily lost in the process of transition under
http://github.com/samtools/htslib[htslib], but will be added back on popular
demand. The original calling model can be invoked with the *-c* option.

==== File format options:

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

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

*-s, --samples* 'FILE'|'LIST'::
    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 

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

*-S, --skip* '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*.

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

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

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

*-p, --pval-threshold* 'float'::
    with *-c*, accept variant if P(ref|D) < 'float'. With *-m*, accept another ALT allele if P(chi^2)>=1-'float'

*-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*)


[[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'::
    what to do with the existing FILTER annotations: use '+' for appending
    to FILTER instead of replacing the existing annotations, and 'x' to 
    reset filters at sites which pass.

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

*-r, --regions* 'file'|'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    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").

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





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

*-a, --all-sites*::
    output for all sites

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

*-G, --GTs-only* 'INT'::
    ignore PLs, use GTs, setting 'INT' for the unseen 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* 'file'|'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    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'|'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
    see *<<common_options,Common Options>>*

==== Output files format:

    CN;;
        This field lists pairwise discordance for all possible sample pairs.
        It is calculated as 
----
        \sum_s { min_{G} \{ PL_i + PL_j \} },
----
    ;;
        where the sum is over all sites 's' and genotype 'G' is selected
        to maximize likelihood for samples 'i' and 'j'. 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.


[[index]]
=== bcftools index ['OPTIONS']  '<in.bcf>|<in.vcf.gz>'
Creates index for bgzip compressed VCF/BCF files for random access. Note 
that the old tabix (.tbi) index can be invoked by setting -m0. Otherwise 
the new coordinate-sorted (.csi) index is created.

*-f, --force*::
    overwrite index if it already exists

*-m, --min-shift 'INT'*::
    set the minimal interval size to 1<<INT; default: 14


[[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

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

*-n, --nfiles* \[+-=]'INT'::
    output positions present in this many (=), this many or more (+), or this
    many or fewer (-) files

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

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

Extract and write records from A shared by both A and B using exact allele match
----
    bcftools isec -p dir -n=2 -w1 A.vcf.gz B.vcf.gz
----

Extract records private to A or B comparing by position only
----
    bcftools isec -p dir -n-1 -c all A.vcf.gz B.vcf.gz 
----


[[merge]]
=== bcftools merge ['OPTIONS'] 'A.vcf.gz' 'B.vcf.gz' [...]
Merge multiple VCF or BCF files 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 create a unique
sample name 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). Sample names
can be also given explicitly using the *--print-header* and
*--use-header* options.


*--use-header* 'FILE'::
    use the VCF header in the provided text 'FILE'

*--print-header*::
    print only merged header and exit

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

*-i, --info-rules* '-'|'TAG:METHOD'[,...]::
    Rules for merging INFO fields (scalars or vectors) or '-' to disable the
    default rules.  'METHOD' is one of 'sum', 'avg', 'min', 'max', 'join'.

*-m, --merge* 'snps'|'indels'|'both'|'all'|'none'::
    Defines  merging behaviour, similar to *-c, --collapse*. For example, to
    prevent merging of SNPs and indels into one record, use *-m* 'both'. To
    prevent creation of multi-allelic records altogether, use *-m* 'none'.

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

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



[[norm]]
=== bcftools norm ['OPTIONS'] *-f* 'ref.fa' 'file.vcf.gz'
Left-align and normalize indels.

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

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

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

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

*-w, --win* 'INT','INT'::
    alignment window and buffer window [50,1000]


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

*-a, --annots* 'LIST'::
    alias for -f '%CHROM\t%POS\t%MASK\t%REF\t%ALT\t%TYPE\t' and tab-separated
    'LIST' of tags

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

*-f, --format* 'FORMAT'::
    learn by example, see below

*-H, --print-header*::
    print header

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

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

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

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

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

==== Format:

    %CHROM          The CHROM column (similarly also other columns, such as POS, ID, QUAL, etc.)
    %INFO/TAG       Any tag in the INFO column
    %TYPE           Variant type (REF, SNP, MNP, INDEL, OTHER)
    %MASK           Indicates presence of the site in other files (with multiple files)
    %TAG{INT}       Curly brackets to subscript vectors (0-based)
    []              The brackets loop over all samples
    %GT             Genotype (e.g. 0/1)
    %TGT            Translated genotype (e.g. C/A)
    %LINE           Prints the whole line
    %SAMPLE         Sample name

==== Examples:

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

[[roh]]
=== bcftools roh 'OPTIONS' 'FILE'
A program for detecting runs of homo/autozygosity.

==== The HMM model:
--------------------------------------
Notation:
  D  = Data, AZ = autozygosity, HW = Hardy-Weinberg (non-autozygosity), 
  f  = non-ref allele frequency

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

Transition probabilities:
  tAZ = P(AZ|HW)  .. from HW to AZ, the -a parameter
  tHW = P(HW|AZ)  .. from AZ to HW, the -H parameter
  P(AZ|AZ) = 1 - P(HW|AZ) = 1 - tHW
  P(HW|HW) = 1 - P(AZ|HW) = 1 - tAZ

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

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

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

==== General Options:

*-b, --biallelic-sites*::
    skip multi-allelic sites, consider only bi-allelic sites

*-e, --estimate-AF* 'all'|'subset'::
    recalculate INFO/AC and INFO/AN on the fly, using either all samples
    ('all') or samples specified via the *-s* option ('subset'). By default,
    allele frequency is estimated from AC and AN counts which are already
    present in the INFO field.

*-F, --AF-tag* 'TAG'|':FILE'::
    use the specified INFO tag 'TAG' as an allele frequency estimate
    instead of the defaul AC and AN tags. Optionally, if prefixed with ':',
    allele frequencies will be read 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 do not have the
    'TAG' or are not present in the 'FILE' or have different reference or
    alternate allele will be skipped. 

*-f, --fwd-bwd*::
    run forward-backward algorithm instead of Viterbi

*-G, --GTs-only* 'FLOAT'::
    use genotypes (FORMAT/GT fields) ignoring genotype likelihoods (FORMAT/PL),
    setting PL of unseen genotypes to 'FLOAT'. Safe value to use is 30 to
    account for GT errors.

*-I, --skip-indels*::
    skip indels as their genotypes are usually enriched for errors

*-m, --genetic-map* 'FILE'::
    genetic map in the format required also by IMPUTE2. Only the first and
    third column are used (position and Genetic_Map(cM)). The 'FILE' can
    be a single file or a file mask, where string "{CHROM}" is replaced with
    chromosome name.

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

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

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

*-w, --win* 'INT'::
    maximum number of sites to keep in memory

==== 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



[[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.

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

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

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

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

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

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

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

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

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

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

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




[[view]]
=== bcftools view 'OPTIONS' 'file.vcf.gz' ['REGION' [...]]
View, subset and filter VCF or BCF files by position and filtering expression.
Convert between VCF and BCF. Former *bcftools subset*.

==== Output options

*-G, --drop-genotypes*::
    drop individual genotype information (after subsetting if *-s* option is set)

*-h, --header-only*:: 
    output the VCF header only

*-H, --no-header*::
    suppress the header in VCF output

*-l, --compression-level* ['0-9']::
    compression level. 0 stands for uncompressed, 1 for best speed and 9 for
    best compression.

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

*-o, --output-file* 'FILE':
    output file name. If not present, the default is to print to standard output (stdout).

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

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


==== Subset options:
*-a, --trim-alt-alleles*::
    trim alternate alleles not seen in subset. Type A, G and R INFO and FORMAT fields will also be trimmed

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

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


==== Filter options:
*-c, --min-ac* 'INT'[':nref'|':alt1'|':minor']::
    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') or minor ('minor') alleles.

*-C, --max-ac* 'INT'[':nref'|':alt1'|':minor']::
    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') or minor ('minor') 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>>*

*-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

*-n, --novel*::
    print novel sites only (ID column is ".")

*-p, --phased*::
    print sites where not 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 not all samples are phased

*-q, --min-af* 'FLOAT'[':nref'|':alt1'|':minor']::
    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') or minor ('minor') alleles.

*-Q, --max-af* 'FLOAT'[':nref'|':alt1'|':minor']::
    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') or minor ('minor') alleles.

*-u, --uncalled*::
    print sites without a called genotype

*-U, --exclude-uncalled*::
    exclude sites without a called genotype

*-v, --types* 'snps'|'indels'|'mnps'|'other'::
    comma-separated list of variant types to select

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

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

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



[[plot-vcfstats]]
=== plot-vcfstats 'OPTIONS' 'file.vchk' [...]
Script for processing output of *<<stats,bcftools stats>>*. It can merge
results from multiple outputs (useful when running the stats for each
chromosome separately), plots graphs and creates a PDF presentation. 

*-m, --merge*::
    Merge vcfstats files to STDOUT, skip plotting.

*-p, --prefix* 'PATH'::
    The output files prefix, add a slash to create new directory.

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

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

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

*-t, --title* 'STRING'::
    Identify files by these titles in plots. The option can be given multiple
    times, for each ID in the *<<stats,bcftools stats>>* output. If not
    present, the script will use abbreviated source file names for the titles.

*-T, --main-title* 'STRING'::
    Main title for the PDF.


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

These filtering expressions are accepted by *<<filter,filter>>* and
*<<view,view>>* commands.

.Valid expressions may contain:

arithmetic perators: ::
    +, *, -, /
    
logical operators: ::
    && (same as &),  || (same as |)
    
comparison operators: ::
    == (same as =), >, >=, <=, <, !=
    
parentheses: ::
    (, )
    
array subscripts to access vector subfields: ::
    e.g. AC[0]
    
double quotes for string values: ::
    e.g. %FILTER="PASS"
    
'1' (or '0') for testing the presence (or absence) of a flag: ::
    e.g. FlagA=1 && FlagB=0
    
'TAG' or INFO/'TAG' for INFO fields: ::
    e.g. DP<800 or INFO/DP<800
    
%'COLUMN' for column names (not all columns are supported yet): ::
    e.g. %QUAL>10 && %FILTER="PASS"
    
%TYPE for testing variant type ('indel', 'snp', 'mnp', 'other'): ::
    e.g. %TYPE="snp"
    
%'FUNC'('TAG') where 'FUNC' is one of 'MAX', 'MIN', 'AVG' and 'TAG' is one of the FORMAT fields: ::
    e.g. %MIN(DP)>10 && %MIN(DV)>3

A few more examples:

    %TYPE="snp" && %QUAL>=10 && (DP4[2]+DP4[3] > 2)
    %MIN(DP)>35 && %AVG(GQ)>50
    ...


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>


COPYING
-------
The MIT License. Copyright (c) Genome Research Ltd.