bcftools.1

'\" t
.\"     Title: bcftools
.\"    Author: [see the "AUTHORS" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\"      Date: 06/12/2014
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "BCFTOOLS" "1" "06/12/2014" "\ \&" "\ \&"
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.SH "NAME"
bcftools \- utilities for variant calling and manipulating VCFs and BCFs
.SH "SYNOPSIS"
.sp
\fBbcftools\fR [\fICOMMAND\fR] [\fIOPTIONS\fR]
.SH "DESCRIPTION"
.sp
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\&.
.sp
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\&.
.sp
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\&.
.SH "LIST OF COMMANDS"
.sp
For a full list of available commands, run \fBbcftools\fR without arguments\&. For a full list of available options, run \fBbcftools\fR \fICOMMAND\fR without arguments\&.
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBindex\fR
\&.\&. index VCF/BCF
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBannotate\fR
\&.\&. edit VCF files, add or remove annotations, apply user plugins
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBcall\fR
\&.\&. SNP/indel calling (former "view")
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBconcat\fR
\&.\&. concatenate VCF/BCF files from the same set of samples
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBfilter\fR
\&.\&. filter VCF/BCF files using fixed thresholds
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBgtcheck\fR
\&.\&. check sample concordance, detect sample swaps and contamination
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBisec\fR
\&.\&. intersections of VCF/BCF files
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBmerge\fR
\&.\&. merge VCF/BCF files files from non\-overlapping sample sets
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBnorm\fR
\&.\&. normalize indels
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBquery\fR
\&.\&. transform VCF/BCF into user\-defined formats
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBroh\fR
\&.\&. identify runs of homo/auto\-zygosity
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBstats\fR
\&.\&. produce VCF/BCF stats (former vcfcheck)
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBview\fR
\&.\&. subset, filter and convert VCF and BCF files
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}

\fBplot\-vcfstats\fR
\&.\&. plots the output of
\fBstats\fR
.RE
.SH "OPTIONS"
.SS "Common Options"
.PP
\fIFILE\fR
.RS 4
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\&.
.RE
.PP
\fB\-c, \-\-collapse\fR \fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIall\fR|\fIsome\fR|\fInone\fR
.RS 4
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 (\fBbcftools isec \-c\fR
\fIall\fR), or only sites with matching variant type (\fBbcftools isec \-c\fR
\fIsnps\fR\ \&
\fB\-c\fR
\fIindels\fR), or only sites with all alleles identical (\fBbcftools isec \-c\fR
\fInone\fR)\&.
.PP
\fInone\fR
.RS 4
only records with identical REF and ALT alleles are compatible
.RE
.PP
\fIsome\fR
.RS 4
only records where some subset of ALT alleles match are compatible
.RE
.PP
\fIall\fR
.RS 4
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\&.
.RE
.PP
\fIsnps\fR
.RS 4
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\&.
.RE
.PP
\fIindels\fR
.RS 4
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\&.
.RE
.PP
\fIboth\fR
.RS 4
abbreviation of "\fB\-c\fR
\fIindels\fR\ \&
\fB\-c\fR
\fIsnps\fR"
.RE
.RE
.PP
\fB\-f, \-\-apply\-filters\fR \fILIST\fR
.RS 4
Skip sites where FILTER column does not contain any of the strings listed in
\fILIST\fR\&. For example, to include only sites which have no filters set, use
\fB\-f\fR
\fI\&.,PASS\fR\&.
.RE
.PP
\fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
.RS 4
Output compressed BCF (\fIb\fR), uncompressed BCF (\fIu\fR), compressed VCF (\fIz\fR), uncompressed VCF (\fIv\fR)\&.
.RE
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
Comma\-separated list of regions, see also
\fB\-R, \-\-regions\-file\fR\&.
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIFILE\fR
.RS 4
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\&.
.RE
.PP
\fB\-s, \-\-samples\fR \fILIST\fR
.RS 4
Comma\-separated list of samples to include
.RE
.PP
\fB\-S, \-\-samples\-file\fR \fIFILE\fR
.RS 4
File of sample names to include, one sample per line\&. The command
\fBbcftools call\fR
accepts an optional second column indicating ploidy (0, 1 or 2) and can parse also PED files\&. With
\fBbcftools call\fR\fB \-C\fR
\fItrio\fR, PED file is expected\&.
.RE
.PP
\fB\-t, \-\-targets\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
Same as
\fB\-r, \-\-regions\fR, but the next position is accessed by streaming the whole VCF/BCF rather than using the tbi/csi index\&. Both
\fB\-r\fR
and
\fB\-t\fR
options can be applied simultaneously:
\fB\-r\fR
uses the index to jump to a region and
\fB\-t\fR
discards positions which are not in the targets\&. Another difference between the two is that
\fB\-r\fR
checks both start and end positions of indels, whereas
\fB\-t\fR
checks start positions only\&.
.RE
.PP
\fB\-T, \-\-targets\-file\fR \fIFILE\fR
.RS 4
Same
\fB\-t, \-\-targets\fR, but reads regions from a file\&.
.RE
.PP
.RS 4
With the
\fBcall \-C\fR
\fIalleles\fR
command, third column of the targets file must be comma\-separated list of alleles, starting with the reference allele\&. Such a file can be easily created from a VCF using:
.RE
.sp
.if n \{\
.RS 4
.\}
.nf
    bcftools query \-f\*(Aq%CHROM\et%POS\et%REF,%ALT\en\*(Aq file\&.vcf
.fi
.if n \{\
.RE
.\}
.SS "bcftools annotate \fI[OPTIONS]\fR \fIFILE\fR"
.sp
This command allows to add or remove annotations and apply user\-written plugins\&.
.PP
\fB\-a, \-\-annotations\fR \fIfile\fR
.RS 4
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
\fB\-c, \-\-columns\fR
and
\fB\-h, \-\-header\-lines\fR\&.
.RE
.PP
\fB\-c, \-\-columns\fR \fIlist\fR
.RS 4
Comma\-separated list of columns present in the annotation file and defined in the header file (see also
\fB\-a, \-\-annotations\fR
and
\fB\-h, \-\-header\-lines\fR)\&. INFO tags can be written both as INFO/TAG or simply TAG\&. Unused columns can be indicated by
\fI\-\fR\&. For example:
.RE
.sp
.if n \{\
.RS 4
.\}
.nf
    CHROM,FROM,TO,REF,ALT,\-,INFO/TAG
.fi
.if n \{\
.RE
.\}
.PP
\fB\-e, \-\-exclude\fR \fIEXPRESSION\fR
.RS 4
exclude sites for which
\fIEXPRESSION\fR
is true\&. For valid expressions see
\fBEXPRESSIONS\fR\&.
.RE
.PP
\fB\-h, \-\-header\-lines\fR \fIfile\fR
.RS 4
Header lines to appended to the VCF header\&.
.RE
.PP
\fB\-i, \-\-include\fR \fIEXPRESSION\fR
.RS 4
include only sites for which
\fIEXPRESSION\fR
is true\&. For valid expressions see
\fBEXPRESSIONS\fR\&.
.RE
.PP
\fB\-l, \-\-list\-plugins\fR
.RS 4
List of available plugins\&. If not installed systemwide, set the environment variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS X) to include directory where
\fBlibths\&.so\fR
is located\&. The BCFTOOLS_PLUGINS environment variable tells the program which directories to search\&.
.RE
.PP
.RS 4
List of plugins coming with the distribution:
.PP
\fBcounts\fR
.RS 4
A minimal plugin which counts number of SNPs, Indels, and total number of sites\&.
.RE
.PP
\fBdosage\fR
.RS 4
Prints genotype dosage determined from tags requested by the user\&. By default the plugin searches for PL, GL and GT (in that order), therefore running
\fB\-p dosage\fR
is equivalent to
\fB\-p dosage:tags=PL,GL,GT\fR\&.
.RE
.PP
\fBfill\-AN\-AC\fR
.RS 4
Fills INFO fields AN and AC\&.
.RE
.PP
\fBframeshifts\fR
.RS 4
Annotate frameshift indels\&. Run as
\fB\-p frameshifts:exons=path/to/file\&.tab\&.gz\fR\&. See the usage of
\fB\-\-targets\-file\fR
above for file format description\&.
.RE
.PP
\fBmissing2ref\fR
.RS 4
Sets missing genotypes ("\&./\&.") to ref allele ("0/0")\&.
.RE
.RE
.PP
\fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-p, \-\-plugins\fR \fIname\fR[:\*(Aqkey\*(Aq=\fIval\fR]
.RS 4
Dynamically loaded plugin to run with optional parameters, see also
\fB\-l, \-\-list\-plugins\fR\&.
.RE
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-x, \-\-remove\fR \fIlist\fR
.RS 4
List of annotations to remove\&. Use
\fIFILTER\fR
to remove all filters or
\fIFILTER/SomeFilter\fR
to remove a specific filter\&. Similarly,
\fIINFO\fR
can be used to remove all INFO tags and
\fIFORMAT\fR
to remove all FORMAT tags except GT\&.
\fIINFO\fR
can be abbreviated to
\fIINF\fR
and
\fIFORMAT\fR
to
\fIFMT\fR\&. A few examples:
.RE
.sp
.if n \{\
.RS 4
.\}
.nf
    ID,INFO/DP,FORMAT/DP
.fi
.if n \{\
.RE
.\}
.PP
\fB\-v, \-\-verbose\fR
.RS 4
print debugging information on plugin failure
.RE
.SS "bcftools call \fI[OPTIONS]\fR \fIFILE\fR"
.sp
This command replaces the former \fBbcftools view\fR caller\&. Some of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand\&. The original calling model can be invoked with the \fB\-c\fR option\&.
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBFile format options:\fR
.RS 4
.PP
\fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-s, \-\-samples\fR \fILIST\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-S, \-\-samples\-file\fR \fIFILE\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-t, \-\-targets\fR \fILIST\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-T, \-\-targets\-file\fR \fIFILE\fR
.RS 4
see
\fBCommon Options\fR
.RE
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBInput/output options:\fR
.RS 4
.PP
\fB\-A, \-\-keep\-alts\fR
.RS 4
output all alternate alleles present in the alignments even if they do not appear in any of the genotypes
.RE
.PP
\fB\-f, \-\-format\-fields\fR \fIlist\fR
.RS 4
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\&.
.RE
.PP
\fB\-M, \-\-keep\-masked\-ref\fR
.RS 4
output sites where REF allele is N
.RE
.PP
\fB\-V, \-\-skip\-variants\fR \fIsnps\fR|\fIindels\fR
.RS 4
skip indel/SNP sites
.RE
.PP
\fB\-v, \-\-variants\-only\fR
.RS 4
output variant sites only
.RE
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBConsensus/variant calling options:\fR
.RS 4
.PP
\fB\-c, \-\-consensus\-caller\fR
.RS 4
the original
\fBsamtools\fR/\fBbcftools\fR
calling method (conflicts with
\fB\-m\fR)
.RE
.PP
\fB\-C, \-\-constrain\fR \fIalleles\fR|\fItrio\fR
.RS 4
.PP
\fIalleles\fR
.RS 4
call genotypes given alleles\&. See also
\fB\-t, \-\-targets\fR\&.
.RE
.PP
\fItrio\fR
.RS 4
call genotypes given the father\-mother\-child constraint\&. See also
\fB\-s, \-\-samples\fR
and
\fB\-n, \-\-novel\-rate\fR\&.
.RE
.RE
.PP
\fB\-m, \-\-multiallelic\-caller\fR
.RS 4
alternative modelfor multiallelic and rare\-variant calling designed to overcome known limitations in
\fB\-c\fR
calling model (conflicts with
\fB\-c\fR)
.RE
.PP
\fB\-n, \-\-novel\-rate\fR \fIfloat\fR[,\&...]
.RS 4
likelihood of novel mutation for constrained
\fB\-C\fR
\fItrio\fR
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=\fIfloat\fR*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\&.
.RE
.PP
\fB\-p, \-\-pval\-threshold\fR \fIfloat\fR
.RS 4
with
\fB\-c\fR, accept variant if P(ref|D) <
\fIfloat\fR\&.
.RE
.PP
\fB\-P, \-\-prior\fR \fIfloat\fR
.RS 4
expected substitution rate, or 0 to disable the prior\&.
.RE
.PP
\fB\-t, \-\-targets\fR \fIfile\fR|\fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-X, \-\-chromosome\-X\fR
.RS 4
haploid output for male samples (requires PED file with
\fB\-s\fR)
.RE
.PP
\fB\-Y, \-\-chromosome\-Y\fR
.RS 4
haploid output for males and skips females (requires PED file with
\fB\-s\fR)
.RE
.RE
.SS "bcftools concat \fI[OPTIONS]\fR \fIFILE1\fR \fIFILE2\fR [\&...]"
.sp
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 \fB\-a, \-\-allow\-overlaps\fR option is specified\&.
.PP
\fB\-a, \-\-allow\-overlaps\fR
.RS 4
First coordinate of the next file can precede last record of the current file\&.
.RE
.PP
\fB\-f, \-\-file\-list\fR \fIFILE\fR
.RS 4
Read the list of files from a file\&.
.RE
.PP
\fB\-l, \-\-ligate\fR
.RS 4
Ligate phased VCFs by matching phase at overlapping haplotypes
.RE
.PP
\fB\-q, \-\-min\-PQ\fR \fIINT\fR
.RS 4
Break phase set if phasing quality is lower than
\fIINT\fR
.RE
.PP
\fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
.RS 4
see
\fBCommon Options\fR
.RE
.SS "bcftools filter \fI[OPTIONS]\fR \fIFILE\fR"
.sp
Apply fixed\-threshold filters\&.
.PP
\fB\-e, \-\-exclude\fR \fIEXPRESSION\fR
.RS 4
exclude sites for which
\fIEXPRESSION\fR
is true\&. For valid expressions see
\fBEXPRESSIONS\fR\&.
.RE
.PP
\fB\-g, \-\-SnpGap\fR \fIINT\fR
.RS 4
filter SNPs within
\fIINT\fR
base pairs of an indel\&. The following example demonstrates the logic of
\fB\-\-SnpGap\fR
\fI3\fR
applied on a deletion and an insertion:
.RE
.sp
.if n \{\
.RS 4
.\}
.nf
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\&.\&.
.fi
.if n \{\
.RE
.\}
.PP
\fB\-G, \-\-IndelGap\fR \fIINT\fR
.RS 4
filter clusters of indels separated by
\fIINT\fR
or fewer base pairs allowing only one to pass\&. The following example demonstrates the logic of
\fB\-\-IndelGap\fR
\fI2\fR
applied on a deletion and an insertion:
.RE
.sp
.if n \{\
.RS 4
.\}
.nf
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\&.\&.
.fi
.if n \{\
.RE
.\}
.PP
\fB\-i, \-\-include\fR \fIEXPRESSION\fR
.RS 4
include only sites for which
\fIEXPRESSION\fR
is true\&. For valid expressions see
\fBEXPRESSIONS\fR\&.
.RE
.PP
\fB\-m, \-\-mode\fR [\fI+x\fR]
.RS 4
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\&.
.RE
.PP
\fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-s, \-\-soft\-filter\fR \fISTRING\fR|\fI+\fR
.RS 4
annotate FILTER column with
\fISTRING\fR
or, with
\fI+\fR, a unique filter name generated by the program ("Filter%d")\&.
.RE
.PP
\fB\-S, \-\-set\-GTs\fR \fI\&.\fR|\fI0\fR
.RS 4
set genotypes of failed samples to missing value (\fI\&.\fR) or reference allele (\fI0\fR)
.RE
.PP
\fB\-t, \-\-targets\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-T, \-\-targets\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.SS "bcftools gtcheck [\fIOPTIONS\fR] [\-g \fIgenotypes\&.vcf\&.gz\fR] \fIquery\&.vcf\&.gz\fR"
.sp
Checks sample identity or, without \fB\-g\fR, multi\-sample cross\-check is performed\&.
.PP
\fB\-a, \-\-all\-sites\fR
.RS 4
output for all sites
.RE
.PP
\fB\-g, \-\-genotypes\fR \fIgenotypes\&.vcf\&.gz\fR
.RS 4
reference genotypes to compare against
.RE
.PP
\fB\-G, \-\-GTs\-only\fR \fIINT\fR
.RS 4
ignore PLs, use GTs, setting
\fIINT\fR
for the unseen genotypes
.RE
.PP
\fB\-H, \-\-homs\-only\fR
.RS 4
consider only genotypes which are homozygous in both
\fIgenotypes\fR
and
\fIquery\fR
VCF\&. This may be useful with low coverage data\&.
.RE
.PP
\fB\-p, \-\-plot\fR \fIPREFIX\fR
.RS 4
produce plots
.RE
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-s, \-\-query\-sample\fR \fISTRING\fR
.RS 4
query sample in
\fIquery\&.vcf\&.gz\fR\&. By default, the first sample is checked\&.
.RE
.PP
\fB\-S, \-\-target\-sample\fR \fISTRING\fR
.RS 4
target sample in the
\fB\-g\fR
file, used only for plotting, not for analysis
.RE
.PP
\fB\-t, \-\-targets\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-T, \-\-targets\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBOutput files format:\fR
.RS 4
.PP
CN, Discordance
.RS 4
Pairwise discordance for all sample pairs is calculated as
.RE
.sp
.if n \{\
.RS 4
.\}
.nf
        \esum_s { min_G { PL_a(G) + PL_b(G) } },
.fi
.if n \{\
.RE
.\}
.PP
.RS 4
where the sum runs over all sites
\fIs\fR
and
\fIG\fR
is the the most likely genotype shared by both samples
\fIa\fR
and
\fIb\fR\&. When PL field is not present, a constant value
\fI99\fR
is used for the unseen genotypes\&. With
\fB\-G\fR, the value
\fI1\fR
can be used instead; the discordance value then gives exactly the number of differing genotypes\&.
.RE
.PP
SM, Average Discordance
.RS 4
Average discordance between sample
\fIa\fR
and all other samples\&.
.RE
.PP
SM, Average Depth
.RS 4
Average depth at evaluated sites, or 1 if FORMAT/DP field is not present\&.
.RE
.PP
SM, Average Number of sites
.RS 4
The average number of sites used to calculate the discordance\&. In other words, the average number of non\-missing PLs/genotypes seen both samples\&.
.RE
.PP
MD, Maximum Deviation
.RS 4
The maximum absolute deviation from average score of the sample most dissimilar to the rest\&.
.RE
.RE
.SS "bcftools index [\fIOPTIONS\fR] \fI<in\&.bcf>|<in\&.vcf\&.gz>\fR"
.sp
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\&.
.PP
\fB\-f, \-\-force\fR
.RS 4
overwrite index if it already exists
.RE
.PP
\fB\-m, \-\-min\-shift \fR\fB\fIINT\fR\fR
.RS 4
set the minimal interval size to 1<<INT; default: 14
.RE
.SS "bcftools isec [\fIOPTIONS\fR] \fIA\&.vcf\&.gz\fR \fIB\&.vcf\&.gz\fR [\&...]"
.sp
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\&.
.PP
\fB\-c, \-\-collapse\fR \fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIall\fR|\fIsome\fR|\fInone\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-C, \-\-complement\fR
.RS 4
output positions present only in the first file but missing in the others
.RE
.PP
\fB\-f, \-\-apply\-filters\fR \fILIST\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-n, \-\-nfiles\fR [+\-=]\fIINT\fR
.RS 4
output positions present in this many (=), this many or more (+), or this many or fewer (\-) files
.RE
.PP
\fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-p, \-\-prefix\fR \fIDIR\fR
.RS 4
if given, subset each of the input files accordingly\&. See also
\fB\-w\fR\&.
.RE
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-t, \-\-targets\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-T, \-\-targets\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-w, \-\-write\fR \fILIST\fR
.RS 4
list of input files to output given as 1\-based indices\&. With
\fB\-p\fR
and no
\fB\-w\fR, all files are written\&.
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBExamples:\fR
.RS 4
.sp
Create intersection and complements of two sets saving the output in dir/*
.sp
.if n \{\
.RS 4
.\}
.nf
    bcftools isec \-p dir A\&.vcf\&.gz B\&.vcf\&.gz
.fi
.if n \{\
.RE
.\}
.sp
Extract and write records from A shared by both A and B using exact allele match
.sp
.if n \{\
.RS 4
.\}
.nf
    bcftools isec \-p dir \-n=2 \-w1 A\&.vcf\&.gz B\&.vcf\&.gz
.fi
.if n \{\
.RE
.\}
.sp
Extract records private to A or B comparing by position only
.sp
.if n \{\
.RS 4
.\}
.nf
    bcftools isec \-p dir \-n\-1 \-c all A\&.vcf\&.gz B\&.vcf\&.gz
.fi
.if n \{\
.RE
.\}
.RE
.SS "bcftools merge [\fIOPTIONS\fR] \fIA\&.vcf\&.gz\fR \fIB\&.vcf\&.gz\fR [\&...]"
.sp
Merge multiple VCF/BCF files from non\-overlapping sample sets to create one multi\-sample file\&. For example, when merging file \fIA\&.vcf\&.gz\fR containing samples \fIS1\fR, \fIS2\fR and \fIS3\fR and file \fIB\&.vcf\&.gz\fR containing samples \fIS3\fR and \fIS4\fR, the output file will contain four samples named \fIS1\fR, \fIS2\fR, \fIS3\fR, \fI2:S3\fR and \fIS4\fR\&.
.sp
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 \fB\-\-force\-samples\fR is given\&. Note that sample names can be also given explicitly using the \fB\-\-print\-header\fR and \fB\-\-use\-header\fR options\&.
.PP
\fB\-\-force\-samples\fR
.RS 4
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
\fI2:S3\fR
in the above example)\&.
.RE
.PP
\fB\-\-print\-header\fR
.RS 4
print only merged header and exit
.RE
.PP
\fB\-\-use\-header\fR \fIFILE\fR
.RS 4
use the VCF header in the provided text
\fIFILE\fR
.RE
.PP
\fB\-f, \-\-apply\-filters\fR \fILIST\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-i, \-\-info\-rules\fR \fI\-\fR|\fITAG:METHOD\fR[,\&...]
.RS 4
Rules for merging INFO fields (scalars or vectors) or
\fI\-\fR
to disable the default rules\&.
\fIMETHOD\fR
is one of
\fIsum\fR,
\fIavg\fR,
\fImin\fR,
\fImax\fR,
\fIjoin\fR\&.
.RE
.PP
\fB\-l, \-\-file\-list\fR \fIFILE\fR
.RS 4
read file names from
\fIFILE\fR
.RE
.PP
\fB\-m, \-\-merge\fR \fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIall\fR|\fInone\fR
.RS 4
Defines merging behaviour, similar to
\fB\-c, \-\-collapse\fR\&. For example, to prevent merging of SNPs and indels into one record, use
\fB\-m\fR
\fIboth\fR\&. To prevent creation of multi\-allelic records altogether, use
\fB\-m\fR
\fInone\fR\&.
.RE
.PP
\fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.SS "bcftools norm [\fIOPTIONS\fR] \-f \fIref\&.fa\fR \fIfile\&.vcf\&.gz\fR"
.sp
Left\-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows\&.
.PP
\fB\-D, \-\-remove\-duplicates\fR
.RS 4
remove duplicate lines of the same type
.RE
.PP
\fB\-f, \-\-fasta\-ref\fR \fIFILE\fR
.RS 4
reference sequence
.RE
.PP
\fB\-m, \-\-multiallelics\fR ←|+>[\fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIany\fR]
.RS 4
split multiallelic sites into biallelic records (\fI\-\fR) or join biallelic sites into multiallelic records (\fI+\fR)\&. 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
\fIsnps\fR; if both SNPs and indels should be merged separately into two records, specify
\fIboth\fR; if SNPs and indels should be merged into a single record, specify
\fIany\fR\&.
.RE
.PP
\fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-t, \-\-targets\fR \fILIST\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-T, \-\-targets\-file\fR \fIFILE\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-w, \-\-site\-win\fR \fIINT\fR
.RS 4
maximum distance between two records to consider when locally sorting variants which changed position during the realignment
.RE
.SS "bcftools query [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR [\fIfile\&.vcf\&.gz\fR [\&...]]"
.sp
Extracts fields from VCF or BCF files and outputs them in user\-defined format\&.
.PP
\fB\-a, \-\-annots\fR \fILIST\fR
.RS 4
alias for \-f
\fI%CHROM\et%POS\et%MASK\et%REF\et%ALT\et%TYPE\et\fR
and tab\-separated
\fILIST\fR
of tags
.RE
.PP
\fB\-c, \-\-collapse\fR \fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIall\fR|\fIsome\fR|\fInone\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-e, \-\-exclude\fR \fIEXPRESSION\fR
.RS 4
exclude sites for which
\fIEXPRESSION\fR
is true\&. For valid expressions see
\fBEXPRESSIONS\fR\&.
.RE
.PP
\fB\-f, \-\-format\fR \fIFORMAT\fR
.RS 4
learn by example, see below
.RE
.PP
\fB\-H, \-\-print\-header\fR
.RS 4
print header
.RE
.PP
\fB\-i, \-\-include\fR \fIEXPRESSION\fR
.RS 4
include only sites for which
\fIEXPRESSION\fR
is true\&. For valid expressions see
\fBEXPRESSIONS\fR\&.
.RE
.PP
\fB\-l, \-\-list\-samples\fR
.RS 4
list sample names and exit
.RE
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-s, \-\-samples\fR \fILIST\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-S, \-\-samples\-file\fR \fIFILE\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-t, \-\-targets\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-T, \-\-targets\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-v, \-\-vcf\-list\fR \fIFILE\fR
.RS 4
process multiple VCFs listed in the file
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBFormat:\fR
.RS 4
.sp
.if n \{\
.RS 4
.\}
.nf
%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
.fi
.if n \{\
.RE
.\}
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBExamples:\fR
.RS 4
.sp
.if n \{\
.RS 4
.\}
.nf
bcftools query \-f \*(Aq%CHROM\et%POS\et%REF\et%ALT[\et%SAMPLE=%GT]\en\*(Aq file\&.vcf\&.gz
.fi
.if n \{\
.RE
.\}
.RE
.SS "bcftools roh \fIOPTIONS\fR \fIFILE\fR"
.sp
A program for detecting runs of homo/autozygosity\&.
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBThe HMM model:\fR
.RS 4
.sp
.if n \{\
.RS 4
.\}
.nf
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}]
.fi
.if n \{\
.RE
.\}
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBGeneral Options:\fR
.RS 4
.PP
\fB\-b, \-\-biallelic\-sites\fR
.RS 4
skip multi\-allelic sites, consider only bi\-allelic sites
.RE
.PP
\fB\-e, \-\-estimate\-AF\fR \fIall\fR|\fIsubset\fR
.RS 4
recalculate INFO/AC and INFO/AN on the fly, using either all samples (\fIall\fR) or samples specified via the
\fB\-s\fR
option (\fIsubset\fR)\&. By default, allele frequency is estimated from AC and AN counts which are already present in the INFO field\&.
.RE
.PP
\fB\-F, \-\-AF\-tag\fR \fITAG\fR|\fI:FILE\fR
.RS 4
use the specified INFO tag
\fITAG\fR
as an allele frequency estimate instead of the defaul AC and AN tags\&. Optionally, if prefixed with
\fI:\fR, allele frequencies will be read from a tab\-delimited file containing the columns: CHROM\etPOS\etREF,ALT\etAF\&. The file can be compressed with
\fBbgzip\fR
and indexed with tabix \-s1 \-b2 \-e2\&. Sites which do not have the
\fITAG\fR
or are not present in the
\fIFILE\fR
or have different reference or alternate allele will be skipped\&.
.RE
.PP
\fB\-f, \-\-fwd\-bwd\fR
.RS 4
run forward\-backward algorithm instead of Viterbi
.RE
.PP
\fB\-G, \-\-GTs\-only\fR \fIFLOAT\fR
.RS 4
use genotypes (FORMAT/GT fields) ignoring genotype likelihoods (FORMAT/PL), setting PL of unseen genotypes to
\fIFLOAT\fR\&. Safe value to use is 30 to account for GT errors\&.
.RE
.PP
\fB\-I, \-\-skip\-indels\fR
.RS 4
skip indels as their genotypes are usually enriched for errors
.RE
.PP
\fB\-m, \-\-genetic\-map\fR \fIFILE\fR
.RS 4
genetic map in the format required also by IMPUTE2\&. Only the first and third column are used (position and Genetic_Map(cM))\&. The
\fIFILE\fR
can chromosome name\&.
.RE
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-s, \-\-samples\fR \fILIST\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-S, \-\-samples\-file\fR \fIFILE\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-t, \-\-targets\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-T, \-\-targets\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-w, \-\-win\fR \fIINT\fR
.RS 4
maximum number of sites to keep in memory
.RE
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBHMM Options:\fR
.RS 4
.PP
\fB\-a, \-\-hw\-to\-az\fR \fIFLOAT\fR
.RS 4
P(AZ|HW) transition probability from AZ (autozygous) to HW (Hardy\-Weinberg) state
.RE
.PP
\fB\-H, \-\-az\-to\-hw\fR \fIFLOAT\fR
.RS 4
P(HW|AZ) transition probability from HW to AZ state
.RE
.RE
.SS "bcftools stats \fIOPTIONS\fR \fIA\&.vcf\&.gz\fR [\fIB\&.vcf\&.gz\fR]"
.sp
Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using \fBplot\-vcfstats\fR\&. When two files are given, the program generates separate stats for intersection and the complements\&.
.PP
\fB\-1, \-\-1st\-allele\-only\fR
.RS 4
consider only 1st allele at multiallelic sites
.RE
.PP
\fB\-c, \-\-collapse\fR \fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIall\fR|\fIsome\fR|\fInone\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-d, \-\-depth\fR \fIINT\fR,\fIINT\fR,\fIINT\fR
.RS 4
ranges of depth distribution: min, max, and size of the bin
.RE
.PP
\fB\-\-debug\fR
.RS 4
produce verbose per\-site and per\-sample output
.RE
.PP
\fB\-e, \-\-exons\fR \fIfile\&.gz\fR
.RS 4
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
.RE
.sp
.if n \{\
.RS 4
.\}
.nf
    tabix \-s1 \-b2 \-e3 file\&.gz
.fi
.if n \{\
.RE
.\}
.PP
\fB\-f, \-\-apply\-filters\fR \fILIST\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-F, \-\-fasta\-ref\fR \fIref\&.fa\fR
.RS 4
faidx indexed reference sequence file to determine INDEL context
.RE
.PP
\fB\-i, \-\-split\-by\-ID\fR
.RS 4
collect stats separately for sites which have the ID column set ("known sites") or which do not have the ID column set ("novel sites")\&.
.RE
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-s, \-\-samples\fR \fILIST\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-S, \-\-samples\-file\fR \fIFILE\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-t, \-\-targets\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-T, \-\-targets\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.SS "bcftools view \fIOPTIONS\fR \fIfile\&.vcf\&.gz\fR [\fIREGION\fR [\&...]]"
.sp
View, subset and filter VCF or BCF files by position and filtering expression\&. Convert between VCF and BCF\&. Former \fBbcftools subset\fR\&.
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBOutput options\fR
.RS 4
.PP
\fB\-G, \-\-drop\-genotypes\fR
.RS 4
drop individual genotype information (after subsetting if
\fB\-s\fR
option is set)
.RE
.PP
\fB\-h, \-\-header\-only\fR
.RS 4
output the VCF header only
.RE
.PP
\fB\-H, \-\-no\-header\fR
.RS 4
suppress the header in VCF output
.RE
.PP
\fB\-l, \-\-compression\-level\fR [\fI0\-9\fR]
.RS 4
compression level\&. 0 stands for uncompressed, 1 for best speed and 9 for best compression\&.
.RE
.PP
\fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
.RS 4
see
\fBCommon Options\fR
.RE
.sp
\fB\-o, \-\-output\-file\fR \fIFILE\fR: output file name\&. If not present, the default is to print to standard output (stdout)\&.
.PP
\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-R, \-\-regions\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-t, \-\-targets\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-T, \-\-targets\-file\fR \fIfile\fR
.RS 4
see
\fBCommon Options\fR
.RE
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBSubset options:\fR
.RS 4
.PP
\fB\-a, \-\-trim\-alt\-alleles\fR
.RS 4
trim alternate alleles not seen in subset\&. Type A, G and R INFO and FORMAT fields will also be trimmed
.RE
.PP
\fB\-I, \-\-no\-update\fR
.RS 4
do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
.RE
.PP
\fB\-s, \-\-samples\fR \fILIST\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-S, \-\-samples\-file\fR \fIFILE\fR
.RS 4
see
\fBCommon Options\fR
.RE
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBFilter options:\fR
.RS 4
.PP
\fB\-c, \-\-min\-ac\fR \fIINT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR]
.RS 4
minimum allele count (INFO/AC) of sites to be printed\&. Specifying the type of allele is optional and can be set to non\-reference (\fInref\fR, the default), 1st alternate (\fIalt1\fR) or minor (\fIminor\fR) alleles\&.
.RE
.PP
\fB\-C, \-\-max\-ac\fR \fIINT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR]
.RS 4
maximum allele count (INFO/AC) of sites to be printed\&. Specifying the type of allele is optional and can be set to non\-reference (\fInref\fR, the default), 1st alternate (\fIalt1\fR) or minor (\fIminor\fR) alleles\&.
.RE
.PP
\fB\-e, \-\-exclude\fR \fIEXPRESSION\fR
.RS 4
exclude sites for which
\fIEXPRESSION\fR
is true\&. For valid expressions see
\fBEXPRESSIONS\fR\&.
.RE
.PP
\fB\-f, \-\-apply\-filters\fR \fILIST\fR
.RS 4
see
\fBCommon Options\fR
.RE
.PP
\fB\-g, \-\-genotypes\fR [^][\fIhom\fR|\fIhet\fR|\fImiss\fR]
.RS 4
include only sites with one or more homozygous (\fIhom\fR), heterozygous (\fIhet\fR) or missing (\fImiss\fR) genotypes\&. When prefixed with
\fI^\fR, the logic is reversed; thus
\fI^het\fR
excludes sites with heterozygous genotypes\&.
.RE
.PP
\fB\-i, \-\-include\fR \fIEXPRESSION\fR
.RS 4
include sites for which
\fIEXPRESSION\fR
is true\&. For valid expressions see
\fBEXPRESSIONS\fR\&.
.RE
.PP
\fB\-k, \-\-known\fR
.RS 4
print known sites only (ID column is not "\&.")
.RE
.PP
\fB\-m, \-\-min\-alleles\fR \fIINT\fR
.RS 4
print sites with at least
\fIINT\fR
alleles listed in REF and ALT columns
.RE
.PP
\fB\-M, \-\-max\-alleles\fR \fIINT\fR
.RS 4
print sites with at most
\fIINT\fR
alleles listed in REF and ALT columns
.RE
.PP
\fB\-n, \-\-novel\fR
.RS 4
print novel sites only (ID column is "\&.")
.RE
.PP
\fB\-p, \-\-phased\fR
.RS 4
print sites where not all samples are phased\&. Haploid genotypes are considered phased\&. Missing genotypes considered unphased unless the phased bit is set\&.
.RE
.PP
\fB\-P, \-\-exclude\-phased\fR
.RS 4
exclude sites where not all samples are phased
.RE
.PP
\fB\-q, \-\-min\-af\fR \fIFLOAT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR]
.RS 4
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 (\fInref\fR, the default), 1st alternate (\fIalt1\fR) or minor (\fIminor\fR) alleles\&.
.RE
.PP
\fB\-Q, \-\-max\-af\fR \fIFLOAT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR]
.RS 4
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 (\fInref\fR, the default), 1st alternate (\fIalt1\fR) or minor (\fIminor\fR) alleles\&.
.RE
.PP
\fB\-u, \-\-uncalled\fR
.RS 4
print sites without a called genotype
.RE
.PP
\fB\-U, \-\-exclude\-uncalled\fR
.RS 4
exclude sites without a called genotype
.RE
.PP
\fB\-v, \-\-types\fR \fIsnps\fR|\fIindels\fR|\fImnps\fR|\fIother\fR
.RS 4
comma\-separated list of variant types to select
.RE
.PP
\fB\-V, \-\-exclude\-types\fR \fIsnps\fR|\fIindels\fR|\fImnps\fR|\fIother\fR
.RS 4
comma\-separated list of variant types to exclude
.RE
.PP
\fB\-x, \-\-private\fR
.RS 4
print sites where only the subset samples carry an non\-reference allele
.RE
.PP
\fB\-X, \-\-exclude\-private\fR
.RS 4
exclude sites where only the subset samples carry an non\-reference allele
.RE
.RE
.SS "plot\-vcfstats \fIOPTIONS\fR \fIfile\&.vchk\fR [\&...]"
.sp
Script for processing output of \fBbcftools stats\fR\&. It can merge results from multiple outputs (useful when running the stats for each chromosome separately), plots graphs and creates a PDF presentation\&.
.PP
\fB\-m, \-\-merge\fR
.RS 4
Merge vcfstats files to STDOUT, skip plotting\&.
.RE
.PP
\fB\-p, \-\-prefix\fR \fIPATH\fR
.RS 4
The output files prefix, add a slash to create new directory\&.
.RE
.PP
\fB\-P, \-\-no\-PDF\fR
.RS 4
Skip the PDF creation step\&.
.RE
.PP
\fB\-r, \-\-rasterize\fR
.RS 4
Rasterize PDF images for faster rendering\&.
.RE
.PP
\fB\-s, \-\-sample\-names\fR
.RS 4
Use sample names for xticks rather than numeric IDs\&.
.RE
.PP
\fB\-t, \-\-title\fR \fISTRING\fR
.RS 4
Identify files by these titles in plots\&. The option can be given multiple times, for each ID in the
\fBbcftools stats\fR
output\&. If not present, the script will use abbreviated source file names for the titles\&.
.RE
.PP
\fB\-T, \-\-main\-title\fR \fISTRING\fR
.RS 4
Main title for the PDF\&.
.RE
.SH "EXPRESSIONS"
.sp
These filtering expressions are accepted by \fBannotate\fR, \fBfilter\fR, \fBquery\fR and \fBview\fR commands\&.
.PP
\fBValid expressions may contain:\fR
.PP
.RS 4
.PP
numerical constants, string constants, file names
.RS 4
1, 1\&.0, 1e\-4 "String" @file_name
.RE
.PP
arithmetic operators
.RS 4
+,*,\-,/
.RE
.PP
comparison operators
.RS 4
== (same as =), >, >=, ⇐, <, !=
.RE
.PP
parentheses
.RS 4
(, )
.RE
.PP
logical operators
.RS 4
&& (same as &), ||, |
.RE
.PP
INFO tags, FORMAT tags, column names
.RS 4
INFO/DP or DP FORMAT/DV, FMT/DV, or DV %FILTER, %QUAL, %ID
.RE
.PP
1 (or 0) to test the presence (or absence) of a flag
.RS 4
FlagA=1 && FlagB=0
.RE
.PP
%TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
.RS 4
%TYPE="indel" | %TYPE="snp"
.RE
.PP
array subscripts
.RS 4
(DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0\&.3
.RE
.PP
functions on FORMAT fields
.RS 4
MAX, MIN, AVG
.RE
.RE
.sp
\fBExamples:\fR
.sp
.if n \{\
.RS 4
.\}
.nf
%MIN(DV)>5
.fi
.if n \{\
.RE
.\}
.sp
.if n \{\
.RS 4
.\}
.nf
%MIN(DV/DP)>0\&.3
.fi
.if n \{\
.RE
.\}
.sp
.if n \{\
.RS 4
.\}
.nf
%MIN(DP)>10 & %MIN(DV)>3
.fi
.if n \{\
.RE
.\}
.sp
.if n \{\
.RS 4
.\}
.nf
%QUAL>10 |  FMT/GQ>10   \&.\&. selects only GQ>10 samples
.fi
.if n \{\
.RE
.\}
.sp
.if n \{\
.RS 4
.\}
.nf
%QUAL>10 || FMT/GQ>10   \&.\&. selects all samples at QUAL>10 sites
.fi
.if n \{\
.RE
.\}
.sp
.if n \{\
.RS 4
.\}
.nf
%TYPE="snp" && %QUAL>=10 && (DP4[2]+DP4[3] > 2)
.fi
.if n \{\
.RE
.\}
.sp
.if n \{\
.RS 4
.\}
.nf
%MIN(DP)>35 && %AVG(GQ)>50
.fi
.if n \{\
.RE
.\}
.sp
.if n \{\
.RS 4
.\}
.nf
%ID=@file       \&.\&. selects lines with ID present in the file
.fi
.if n \{\
.RE
.\}
.sp
.if n \{\
.RS 4
.\}
.nf
%ID!=@~/file    \&.\&. skip lines with ID present in the ~/file
.fi
.if n \{\
.RE
.\}
.sp
\fBShell expansion:\fR
.sp
Note that expressions must often be quoted because some characters have special meaning in the shell\&. Please refer to the documentation of your shell for details\&. An example of expression enclosed in single quotes which cause that the whole expression is passed to the program as intended:
.sp
.if n \{\
.RS 4
.\}
.nf
bcftools view \-i \*(Aq%ID!="\&." & MAF[0]<0\&.01\*(Aq
.fi
.if n \{\
.RE
.\}
.SH "PERFORMANCE"
.sp
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 \fBawk\fR or \fBcut\fR\&. Therefore it is recommended to use BCF as input/output format whenever possible to avoid large overhead of the VCF → BCF → VCF conversion\&.
.SH "BUGS"
.sp
Please report any bugs you encounter on the github website: http://github\&.com/samtools/bcftools
.SH "AUTHORS"
.sp
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\&.
.SH "RESOURCES"
.sp
Bcftools GitHub website: http://github\&.com/samtools/bcftools
.sp
Samtools GitHub website: http://github\&.com/samtools/samtools
.sp
HTSlib GitHub website: http://github\&.com/samtools/htslib
.sp
File format specifications: http://samtools\&.github\&.io/hts\-specs
.sp
Bcftools documentation: http://samtools\&.github\&.io/bcftools
.sp
Bcftools wiki page: https://github\&.com/samtools/bcftools/wiki
.SH "COPYING"
.sp
The MIT License\&. Copyright (c) Genome Research Ltd\&.