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bcftools(1)

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 2016-04-18 14:18 BST and refers to
   bcftools git version 1.3-36-g47e811c+.

   BCF1
   The BCF1 format output by versions of samtools <= 0.1.19 is not
   compatible with this version of bcftools. To read BCF1 files one can
   use the view command from old versions of bcftools packaged with
   samtools versions <= 0.1.19 to convert to VCF, which can then be read
   by this version of bcftools.

           samtools-0.1.19/bcftools/bcftools view file.bcf1 | bcftools view

   VARIANT CALLING
   See bcftools call for variant calling from the output of the samtools
   mpileup command. In versions of samtools <= 0.1.19 calling was done
   with bcftools view. Users are now required to choose between the old
   samtools calling model (-c/--consensus-caller) and the new multiallelic
   calling model (-m/--multiallelic-caller). The multiallelic calling
   model is recommended for most tasks.

LIST OF COMMANDS

   For a full list of available commands, run bcftools without arguments.
   For a full list of available options, run bcftools COMMAND without
   arguments.

   *    annotate .. edit VCF files, add or remove annotations

   *    call .. SNP/indel calling (former "view")

   *    cnv .. Copy Number Variation caller

   *    concat .. concatenate VCF/BCF files from the same set of samples

   *    consensus .. create consensus sequence by applying VCF variants

   *    convert .. convert VCF/BCF to other formats and back

   *    filter .. filter VCF/BCF files using fixed thresholds

   *    gtcheck .. check sample concordance, detect sample swaps and
       contamination

   *    index .. index VCF/BCF

   *    isec .. intersections of VCF/BCF files

   *    merge .. merge VCF/BCF files files from non-overlapping sample
       sets

   *    norm .. normalize indels

   *    plugin .. run user-defined plugin

   *    polysomy .. detect contaminations and whole-chromosome aberrations

   *    query .. transform VCF/BCF into user-defined formats

   *    reheader .. modify VCF/BCF header, change sample names

   *    roh .. identify runs of homo/auto-zygosity

   *    stats .. produce VCF/BCF stats (former vcfcheck)

   *    view .. subset, filter and convert VCF and BCF files

LIST OF SCRIPTS

   Some helper scripts are bundled with the bcftools code.

   *    plot-vcfstats .. plots the output of stats

COMMANDS AND OPTIONS

Common Options
The following options are common to many bcftools commands. See usage
for specific commands to see if they apply.

FILE
Files can be both VCF or BCF, uncompressed or BGZF-compressed. The
file "-" is interpreted as standard input. Some tools may require
tabix- or CSI-indexed files.

-c, --collapse snps|indels|both|all|some|none|id
Controls how to treat records with duplicate positions and defines
compatible records across multiple input files. Here by
"compatible" we mean records which should be considered as
identical by the tools. For example, when performing line
intersections, the desire may be to consider as identical all sites
with matching positions (bcftools isec -c all), or only sites with
matching variant type (bcftools isec -c snps -c indels), or only
sites with all alleles identical (bcftools isec -c none).

none
only records with identical REF and ALT alleles are compatible

some
only records where some subset of ALT alleles match are
compatible

all
all records are compatible, regardless of whether the ALT
alleles match or not. In the case of records with the same
position, only the first will be considered and appear on
output.

snps
any SNP records are compatible, regardless of whether the ALT
alleles match or not. For duplicate positions, only the first
SNP record will be considered and appear on output.

indels
all indel records are compatible, regardless of whether the REF
and ALT alleles match or not. For duplicate positions, only the
first indel record will be considered and appear on output.

both
abbreviation of "-c indels -c snps"

id
only records with identical ID column are compatible. Supported
by bcftools merge only.

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

--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 VCFBCF 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 [^]LIST
Comma-separated list of samples to include or exclude if prefixed
with "^". Note that in general tags such as INFO/AC, INFO/AN, etc
are not updated to correspond to the subset samples. bcftools view
is the exception where some tags will be updated (unless the -I,
--no-update option is used; see 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 FILE
File of sample names to include or exclude if prefixed with "^".
One sample per line. See also the note above for the -s, --samples
option. The command bcftools call accepts an optional second column
indicating ploidy (0, 1 or 2) or sex (as defined by --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 bcftools call
-C trio, PED file is expected. File formats examples:

sample1 1
sample2 2
sample3 2

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 [^]chr|chr:pos|chr:from-to|chr:from-[,...]
Similar as -r, --regions, but the next position is accessed by
streaming the whole VCF/BCF rather than using the tbi/csi index.
Both -r and -t options can be applied simultaneously: -r uses the
index to jump to a region and -t discards positions which are not
in the targets. Unlike -r, targets can be prefixed with "^" to
request logical complement. For example, "^X,Y,MT" indicates that
sequences X, Y and MT should be skipped. Yet another difference
between the two is that -r checks both start and end positions of
indels, whereas -t checks start positions only. Note that -t cannot
be used in combination with -T.

-T, --targets-file [^]FILE
Same -t, --targets, but reads regions from a file. Note that -T
cannot be used in combination with -t.

With the call -C alleles command, third column of the targets file
must be comma-separated list of alleles, starting with the
reference allele. 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.

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.

-c, --columns list
Comma-separated list of columns or tags to carry over from the
annotation file (see also -a, --annotations). If the annotation
file is not a VCF/BCF, list describes the columns of the annotation
file and must include CHROM, POS (or, alternatively, FROM and TO),
and optionally REF and ALT. Unused columns which should be ignored
can be indicated by "-". If the annotation file is a VCF/BCF, only
the edited columns/tags must be present and their order does not
matter. The columns ID, QUAL, FILTER, INFO and FORMAT can be
edited, where INFO tags can be written both as "INFO/TAG" or simply
"TAG", and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG".
To carry over all INFO annotations, use "INFO". To add all INFO
annotations except "TAG", use "^INFO/TAG". By default, existing
values are replaced. To add 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.

-h, --header-lines file
Lines to append to the VCF header, see also -c, --columns and -a,
--annotations. For example:

##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">

-I, --set-id [+]FORMAT
assign ID on the fly. The format is the same as in the query
command (see below). By default all existing IDs are replaced. If
the format string is preceded by "+", only missing IDs will be set.
For example, one can use

bcftools annotate --set-id +'%CHROM\_%POS\_%REF\_%FIRST_ALT' file.vcf

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid
expressions see EXPRESSIONS.

-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

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
see Common Options

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--rename-chrs file
rename chromosomes according to the map in file, with "old_name
new_name\n" pairs separated by whitespaces, each on a separate
line.

-s, --samples [^]LIST
subset of samples to annotate, see also Common Options

-S, --samples-file FILE
subset of samples to annotate. If the samples are named differently
in the target VCF and the -a, --annotations VCF, the name mapping
can be given as "src_name dst_name\n", separated by whitespaces,
each pair on a separate line.

--threads INT
see 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 "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and
FILTER). "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".

Examples:

# Remove three fields
bcftools annotate -x ID,INFO/DP,FORMAT/DP file.vcf.gz

# Remove all INFO fields and all FORMAT fields except for GT and PL
bcftools annotate -x INFO,^FORMAT/GT,FORMAT/PL file.vcf

# Add ID, QUAL and INFO/TAG, not replacing TAG if already present
bcftools annotate -a src.bcf -c ID,QUAL,+TAG dst.bcf

# Carry over all INFO and FORMAT annotations except FORMAT/GT
bcftools annotate -a src.bcf -c INFO,^FORMAT/GT dst.bcf

# Annotate from a tab-delimited file with six columns (the fifth is ignored),
# first indexing with tabix. The coordinates are 1-based.
tabix -s1 -b2 -e2 annots.tab.gz
bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,POS,REF,ALT,-,TAG file.vcf

# Annotate from a tab-delimited file with regions (1-based coordinates, inclusive)
tabix -s1 -b2 -e3 annots.tab.gz
bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG inut.vcf

# Annotate from a bed file (0-based coordinates, half-closed, half-open intervals)
bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf

bcftools 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

-R, --regions-file file
see Common Options

-s, --query-sample string
query samply name

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see 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.

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

File format options:
--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
see Common Options

--ploidy ASSEMBLY[?]
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. 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

-R, --regions-file file
see Common Options

-s, --samples LIST
see Common Options

-S, --samples-file FILE
see Common Options

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see Common Options

--threads INT
see Common Options

Input/output options:
-A, --keep-alts
output all alternate alleles present in the alignments even if
they do not appear in any of the genotypes

-f, --format-fields list
comma-separated list of FORMAT fields to output for each
sample. Currently GQ and GP fields are supported. For
convenience, the fields can be given as lower case letters.

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

-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.

-t, --targets file|chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-X, --chromosome-X
haploid output for male samples (requires PED file with -s)

-Y, --chromosome-Y
haploid output for males and skips females (requires PED file
with -s)

bcftools concat [OPTIONS] FILE1 FILE2 [...]
Concatenate or combine VCF/BCF files. All source files must have the
same sample columns appearing in the same order. Can be used, for
example, to concatenate chromosome VCFs into one VCF, or combine a SNP
VCF and an indel VCF into one. The input files must be sorted by chr
and position. The files must be given in the correct order to produce
sorted VCF on output unless the -a, --allow-overlaps option is
specified. 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 the list of files from a file.

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

--no-version
see Common Options

-n, --naive
Concatenate BCF files without recompression. This is very fast but
requires that all files 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 and only works for compressed BCF files.
Dangerous, use with caution.

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
see Common Options

-q, --min-PQ INT
Break phase set if phasing quality is lower than INT

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options. Requires -a, --allow-overlaps.

-R, --regions-file FILE
see Common Options. Requires -a, --allow-overlaps.

--threads INT
see Common Options

bcftools consensus [OPTIONS] FILE
Create consensus sequence by applying VCF variants to a reference fasta
file.

-f, --fasta-ref FILE
reference sequence in fasta format

-H, --haplotype 1|2
apply variants for the given haplotype. This option requires -s,
unless exactly one sample is present in the VCF

-i, --iupac-codes
output variants in the form of IUPAC ambiguity codes

-m, --mask FILE
BED file or TAB file with regions to be replaced with N. See
discussion of --regions-file in Common Options for file format
details.

-o, --output FILE
write output to a file

-s, --sample NAME
apply variants of the given sample

Examples:

# Apply variants present in sample "NA001", output IUPAC codes for hets
bcftools consensus -i -s NA001 -f in.fa in.vcf.gz > out.fa

# Create consensus for one region. The fasta header lines are then expected
# in the form ">chr:from-to".
samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz -o out.fa

bcftools convert [OPTIONS] FILE
VCF input options:
-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid
expressions see EXPRESSIONS.

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid
expressions see EXPRESSIONS.

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file FILE
see Common Options

-s, --samples LIST
see Common Options

-S, --samples-file FILE
see Common Options

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see Common Options

VCF output options:
--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
see Common Options

--threads INT
see Common Options

GEN/SAMPLE conversion:
-G, --gensample2vcf prefix or gen-file,sample-file
convert IMPUTE2 output to VCF. The second column must be of the
form "CHROM:POS_REF_ALT" to detect possible strand swaps;
IMPUTE2 leaves the first one empty ("--") when sites from
reference panel are filled in. See also -g below.

-g, --gensample prefix or gen-file,sample-file
convert from VCF to gen/sample format used by IMPUTE2 and
SHAPEIT. The columns of .gen file format are ID1,ID2,POS,A,B
followed by three genotype probabilities P(AA), P(AB), P(BB)
for each sample. In order to prevent strand swaps, the program
uses IDs of the form "CHROM:POS_REF_ALT". For example:

.gen
----
1:111485207_G_A 1:111485207_G_A 111485207 G A 0 1 0 0 1 0
1:111494194_C_T 1:111494194_C_T 111494194 C T 0 1 0 0 0 1

.sample
-------
ID_1 ID_2 missing
0 0 0
sample1 sample1 0
sample2 sample2 0

--tag STRING
tag to take values for .gen file: GT,PL,GL,GP

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

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

HAPS/SAMPLE conversion:
--hapsample2vcf prefix or haps-file,sample-file
convert from haps/sample format to VCF. The columns of .haps
file are similar to .gen file above, but there are only two
haplotype columns per sample. Note that the first column of the
haps file is expected to be in the form
"CHR:POS_REF_ALT(_END)?", with the _END being optional for
defining the INFO/END tag when ALT is a symbolic allele, for
example:

.haps
----
1:111485207_G_A rsID1 111485207 G A 0 1 0 0
1:111494194_C_T rsID2 111494194 C T 0 1 0 0
1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0

--hapsample prefix or haps-file,sample-file
convert from VCF to haps/sample format used by IMPUTE2 and
SHAPEIT. The columns of .haps 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.

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

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

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

.haps
-----
0 1 0 0 1 0
0 1 0 0 0 1

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

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

--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

-S, --samples-file FILE
file of sample names. See Common Options

Example:

# Convert 23andme results into VCF
bcftools convert -c ID,CHROM,POS,AA -s SampleName -f 23andme-ref.fa --tsv2vcf 23andme.txt -Oz -o out.vcf.gz

bcftools filter [OPTIONS] FILE
Apply fixed-threshold filters.

-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions
see EXPRESSIONS.

-g, --SnpGap INT
filter SNPs within INT base pairs of an indel. The following
example demonstrates the logic of --SnpGap 3 applied on a deletion
and an insertion:

The SNPs at positions 1 and 7 are filtered, positions 0 and 8 are not:
0123456789
ref .G.GT..G..
del .A.G-..A..
Here the positions 1 and 6 are filtered, 0 and 7 are not:
0123-456789
ref .G.G-..G..
ins .A.GT..A..

-G, --IndelGap INT
filter clusters of indels separated by INT or fewer base pairs
allowing only one to pass. The following example demonstrates the
logic of --IndelGap 2 applied on a deletion and an insertion:

The second indel is filtered:
012345678901
ref .GT.GT..GT..
del .G-.G-..G-..
And similarly here, the second is filtered:
01 23 456 78
ref .A-.A-..A-..
ins .AT.AT..AT..

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid
expressions see EXPRESSIONS.

-m, --mode [+x]
define behaviour at sites with existing FILTER annotations. The
default mode replaces existing filters of failed sites with a new
FILTER string while leaving sites which pass untouched when
non-empty and setting to "PASS" when the FILTER string is absent.
The "+" mode appends new FILTER strings of failed sites instead of
replacing them. The "x" mode resets filters of sites which pass to
"PASS". Modes "+" and "x" can both be set.

--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
see Common Options

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

-s, --soft-filter STRING|+
annotate FILTER column with STRING or, with +, a unique filter name
generated by the program ("Filter%d").

-S, --set-GTs .|0
set genotypes of failed samples to missing value (.) or reference
allele (0)

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

--threads INT
see Common Options

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

-a, --all-sites
output for all sites

-g, --genotypes genotypes.vcf.gz
reference genotypes to compare against

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

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

-p, --plot PREFIX
produce plots

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

-s, --query-sample STRING
query sample in query.vcf.gz. By default, the first sample is
checked.

-S, --target-sample STRING
target sample in the -g file, used only for plotting, not for
analysis

-t, --targets file
see Common Options

-T, --targets-file file
see Common Options

Output files format:
CN, Discordance
Pairwise discordance for all sample pairs is calculated as

\sum_s { min_G { PL_a(G) + PL_b(G) } },

where the sum runs over all sites s and G is the the most
likely genotype shared by both samples a and b. When PL field
is not present, a constant value 99 is used for the unseen
genotypes. With -G, the value 1 can be used instead; the
discordance value then gives exactly the number of differing
genotypes.

SM, Average Discordance
Average discordance between sample a and all other samples.

SM, Average Depth
Average depth at evaluated sites, or 1 if FORMAT/DP field is
not present.

SM, Average Number of sites
The average number of sites used to calculate the discordance.
In other words, the average number of non-missing PLs/genotypes
seen both samples.

bcftools index [OPTIONS] <in.bcf>|<in.vcf.gz>
Creates index for bgzip compressed VCF/BCF files for random access. CSI
(coordinate-sorted index) is created by default. The CSI format
supports indexing of chromosomes up to length 2^31. TBI (tabix index)
index files, which support chromosome lengths up to 2^29, can be
created by using the -t/--tbi option or using the tabix program
packaged with htslib. When loading an index file, bcftools will try the
CSI first and then the TBI.

Indexing options:
-c, --csi
generate CSI-format index for VCF/BCF files [default]

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

-m, --min-shift INT
set minimal interval size for CSI indices to 2^INT; default: 14

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

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

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

bcftools isec [OPTIONS] A.vcf.gz B.vcf.gz [...]
Creates intersections, unions and complements of VCF files. Depending
on the options, the program can output records from one (or more) files
which have (or do not have) corresponding records with the same
position in the other files.

-C, --complement
output positions present only in the first file but missing in the
others

-e, --exclude -|EXPRESSION
exclude sites for which EXPRESSION is true. If -e (or -i) appears
only once, the same filtering expression will be applied to all
input files. Otherwise, -e or -i must be given for each input file.
To indicate that no filtering should be performed on a file, use
"-" in place of EXPRESSION, as shown in the example below. For
valid expressions see EXPRESSIONS.

-f, --apply-filters LIST
see Common Options

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. See discussion of
-e, --exclude above.

-n, --nfiles [+-=]INT|~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. When several files are being output, their
names are controlled via -p instead.

-O, --output-type b|u|z|v
see Common Options

-p, --prefix DIR
if given, subset each of the input files accordingly. See also -w.

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

-w, --write LIST
list of input files to output given as 1-based indices. With -p and
no -w, all files are written.

Examples:
Create intersection and complements of two sets saving the output
in dir/*

bcftools isec -p dir A.vcf.gz B.vcf.gz

Filter sites in A and B (but not in C) and create intersection

bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e- A.vcf.gz B.vcf.gz C.vcf.gz -p dir

Extract and write records from A shared by both A and B using exact
allele match

bcftools isec -p dir -n=2 -w1 A.vcf.gz B.vcf.gz

Extract records private to A or B comparing by position only

bcftools isec -p dir -n-1 -c all A.vcf.gz B.vcf.gz

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

bcftools merge [OPTIONS] A.vcf.gz B.vcf.gz [...]
Merge multiple VCF/BCF files from non-overlapping sample sets to create
one multi-sample file. For example, when merging file A.vcf.gz
containing samples S1, S2 and S3 and file B.vcf.gz containing samples
S3 and S4, the output file will contain four samples named S1, S2, S3,
2:S3 and S4.

Note that it is responsibility of the user to ensure that the sample
names are unique across all files. If they are not, the program will
exit with an error unless the option --force-samples is given. The
sample names can be also given explicitly using the --print-header and
--use-header options.

Note that only records from different files can be merged, never from
the same file. For "vertical" merge take a look at bcftools norm
instead.

--force-samples
if the merged files contain duplicate samples names, proceed
anyway. Duplicate sample names will be resolved by prepending index
of the file as it appeared on the command line to the conflicting
sample name (see 2:S3 in the above example).

--print-header
print only merged header and exit

--use-header FILE
use the VCF header in the provided text FILE

-f, --apply-filters LIST
see Common Options

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

-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

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
see Common Options

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

--threads INT
see Common Options

bcftools norm [OPTIONS] file.vcf.gz
Left-align and normalize indels, check if REF alleles match the
reference, split multiallelic sites into multiple rows; recover
multiallelics from multiple rows. Left-alignment and normalization will
only be applied if the --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|all|none
If a record is present in multiple files, output only the first
instance, see --collapse in Common Options. Requires -a,
--allow-overlaps.

-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
reference sequence. Supplying this option will turn on
left-alignment and normalization, however, see also the
--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

-N, --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

-O, --output-type b|u|z|v
see Common Options

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

-s, --strict-filter
when merging (-m+), merged site is PASS only if all sites being
merged PASS

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see Common Options

--threads INT
see Common Options

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

bcftools [plugin NAME|+NAME] [OPTIONS] FILE --- [PLUGIN OPTIONS]
VCF input options:
-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid
expressions see EXPRESSIONS.

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid
expressions see EXPRESSIONS.

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

VCF output options:
--no-version
see Common Options

-o, --output FILE
see Common Options

-O, --output-type b|u|z|v
see Common Options

--threads INT
see 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.

If htslib is not installed systemwide, set the environment
variable LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (Mac OS
X) to include the directory where libhts.so.1 is located.

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

-V, --version
print version string and exit

List of plugins coming with the distribution:
counts
a minimal plugin which counts number of SNPs, Indels, and total
number of sites.

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

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

fix-ploidy
sets correct ploidy

frameshifts
annotate frameshift indels

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

tag2tag
Convert between similar tags, such as GL and GP.

vcf2sex
determine sample sex by checking genotypes in haploid regions

Examples:
# List options common to all plugins
bcftools plugin

# List available plugins
bcftools plugin -l

# 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?

* Are all shared libraries, namely libhts.so, accessible? Verify
with

* on Mac OS X: otool -L your/plugin.so and set
DYLD_LIBRARY_PATH if they are not

* on Linux: ldd your/plugin.so and set LD_LIBRARY_PATH if
they are not

* If not installed systemwide, set the environment variable
LD_LIBRARY_PATH (linux) or DYLD_LIBRARY_PATH (mac) to include
directory where libhts.so is located.

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

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

// Called once at startup, allows 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);

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

-R, --regions-file file
see Common Options

-s, --sample string
sample name

-t, --targets LIST
see Common Options

-T, --targets-file FILE
see 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

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.

-f, --format FORMAT
learn by example, see below

-H, --print-header
print header

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid
expressions see EXPRESSIONS.

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

-o, --output FILE
see Common Options

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

-s, --samples LIST
see Common Options

-S, --samples-file FILE
see Common Options

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

-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, OTHER)
%MASK Indicates presence of the site in other files (with multiple files)
%TAG{INT} Curly brackets to subscript vectors (0-based)
%FIRST_ALT Alias for %ALT{0}
[] The brackets loop over all samples
%GT Genotype (e.g. 0/1)
%TGT Translated genotype (e.g. C/A)
%IUPACGT Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
%LINE Prints the whole line
%SAMPLE Sample name

Examples:
bcftools query -f '%CHROM %POS %REF %ALT{0}\n' file.vcf.gz
bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz

bcftools reheader [OPTIONS] file.vcf.gz
Modify header of VCF/BCF files, change sample names.

-h, --header FILE
new VCF header

-o, --output FILE
see Common Options

-s, --samples FILE
new sample names, one name per line, in the same order as they
appear in the VCF file. Alternatively, only samples which need to
be renamed can be listed as "old_name new_name\n" pairs separated
by whitespaces, each on 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".

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

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

-e, --estimate-AF FILE
recalculate INFO/AC and INFO/AN on the fly, using either all
samples ("-") or samples listed in FILE. By default, allele
frequency is estimated from AC and AN counts which are already
present in the INFO field.

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

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

-m, --genetic-map FILE
genetic map in the format required also by IMPUTE2. Only the
first and third column are used (position and Genetic_Map(cM)).
The FILE can chromosome name.

-M, --rec-rate FLOAT
constant recombination rate per bp

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

-s, --sample name
the name of sample to analyze

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

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

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

-V, --viterbi-training
perform Viterbi training to estimate transition probabilities

bcftools stats [OPTIONS] A.vcf.gz [B.vcf.gz]
Parses VCF or BCF and produces text file stats which is suitable for
machine processing and can be plotted using plot-vcfstats. When two
files are given, the program generates separate stats for intersection
and the complements. By default only sites are compared, -s/-S must
given to include also sample columns.

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

-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.

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

tabix -s1 -b2 -e3 file.gz

-f, --apply-filters LIST
see Common Options

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

-i, --include EXPRESSION
include only sites for which EXPRESSION is true. For valid
expressions see 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

-R, --regions-file file
see Common Options

-s, --samples LIST
see Common Options

-S, --samples-file FILE
see Common Options

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

-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

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

-O, --output-type b|u|z|v
see Common Options

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

-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-R, --regions-file file
see Common Options

-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options

-T, --targets-file file
see Common Options

--threads INT
see Common Options

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

--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

-S, --samples-file FILE
see 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.

-f, --apply-filters LIST
see Common Options

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

-i, --include EXPRESSION
include sites for which EXPRESSION is true. For valid
expressions see EXPRESSIONS.

-k, --known
print known sites only (ID column is not ".")

-m, --min-alleles INT
print sites with at least INT alleles listed in REF and ALT
columns

-M, --max-alleles INT
print sites with at most INT alleles listed in REF and ALT
columns. Use -m2 -M2 -v snps to only view biallelic SNPs.

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

-p, --phased
print sites where all samples are phased. Haploid genotypes are
considered phased. Missing genotypes considered unphased unless
the phased bit is set.

-P, --exclude-phased
exclude sites where all samples are phased

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

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

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

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

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

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.

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

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

EXPRESSIONS

   These filtering expressions are accepted by annotate, filter, query and
   view commands.

   Valid expressions may contain:

   *   numerical constants, string constants, file names

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

   *   arithmetic operators

           +,*,-,/

   *   comparison operators

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

   *   regex operators "~" and its negation "!~"

           INFO/HAYSTACK ~ "needle"

   *   parentheses

           (, )

   *   logical operators

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

   *   INFO tags, FORMAT tags, column names

           INFO/DP or DP
           FORMAT/DV, FMT/DV, or DV
           FILTER, QUAL, ID, 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 this expression

           GT="."

   *   TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)

           TYPE="indel" | TYPE="snp"

   *   array subscripts, "*" for any field

           (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
           DP4[*] == 0
           CSQ[*] ~ "missense_variant.*deleterious"

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

           MAX, MIN, AVG, SUM, STRLEN, ABS

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

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

   Notes:

   *   String comparisons and regular expressions are case-insensitive

   *   If the subscript "*" is used in regular expression search, the
       whole field is treated as one string. For example, the regex
       STR[*]~"B,C" will be true for the string vector INFO/STR=AB,CD.

   *   Variables and function names are case-insensitive, but not tag
       names. For example, "qual" can be used instead of "QUAL",
       "strlen()" instead of "STRLEN()" , but not "dp" instead of "DP".

   Examples:

       MIN(DV)>5

       MIN(DV/DP)>0.3

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

       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   .. selects only GQ>10 samples

       QUAL>10 || FMT/GQ>10   .. selects all samples at QUAL>10 sites

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

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

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

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

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

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

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

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

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

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

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

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

   -T, --main-title STRING
       Main title for the PDF.

PERFORMANCE

   HTSlib was designed with BCF format in mind. When parsing VCF files,
   all records are internally converted into BCF representation. Simple
   operations, like removing a single column from a VCF file, can be
   therefore done much faster with standard UNIX commands, such as awk or
   cut. Therefore it is recommended to use BCF as input/output format
   whenever possible to avoid large overhead of the VCF  BCF  VCF
   conversion.

BUGS

   Please report any bugs you encounter on the github website:
   http://github.com/samtools/bcftools

AUTHORS

   Heng Li from the Sanger Institute wrote the original C version of
   htslib, samtools and bcftools. Bob Handsaker from the Broad Institute
   implemented the BGZF library. Petr Danecek, Shane McCarthy and John
   Marshall are maintaining and further developing bcftools. Many other
   people contributed to the program and to the file format
   specifications, both directly and indirectly by providing patches,
   testing and reporting bugs. We thank them all.

RESOURCES

   BCFtools GitHub website: http://github.com/samtools/bcftools

   Samtools GitHub website: http://github.com/samtools/samtools

   HTSlib GitHub website: http://github.com/samtools/htslib

   File format specifications: http://samtools.github.io/hts-specs

   BCFtools documentation: http://samtools.github.io/bcftools

   BCFtools wiki page: https://github.com/samtools/bcftools/wiki

COPYING

   The MIT/Expat License or GPL License, see the LICENSE document for
   details. Copyright (c) Genome Research Ltd.

                         2016-04-18 14:18 BST                  BCFTOOLS(1)

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