bcftools(1) 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 VCF←→BCF conversion.

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

Comma-separated list of regions, see also -R, --regions-file. Note that -r cannot be used in combination with -R.

-R, --regions-file FILE

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

-s, --samples [^]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
  or
    sample1    M
    sample2    F
    sample3    F
  or a .ped file (here is shown a minimum working example, the first column is
  ignored and the last indicates sex: 1=male, 2=female)
    ignored daughterA fatherA motherA 2
    ignored sonB fatherB motherB 1

-t, --targets [^]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

--haploid2diploid

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

--vcf-ids

output VCF IDs instead of "CHROM:POS_REF_ALT" IDs


TSV conversion:

--tsv2vcf file

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

-c, --columns list

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

-f, --fasta-ref file

reference sequence in fasta format. 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, --collapse snps|indels|both|all|some|none

see Common Options

-C, --complement

output positions present only in the first file but missing in the others

-e, --exclude -|EXPRESSION

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

-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, --merge snps|indels|both|all|none|id

The option controls what types of multiallelic records can be created: 

-m none   ..  no new multiallelics, output multiple records instead
-m snps   ..  allow multiallelic SNP records
-m indels ..  allow multiallelic indel records
-m both   ..  both SNP and indel records can be multiallelic
-m all    ..  SNP records can be merged with indel records
-m id     ..  merge by ID

--no-version

see Common Options

-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.

-c, --collapse snps|indels|both|all|some|none

see Common Options

-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
Emission probabilities:
  oAZ = P_i(D|AZ) = (1-f)*P(D|RR) + f*P(D|AA)
  oHW = P_i(D|HW) = (1-f)^2 * P(D|RR) + f^2 * P(D|AA) + 2*f*(1-f)*P(D|RA)
Transition probabilities:
  tAZ = P(AZ|HW)  .. from HW to AZ, the -a parameter
  tHW = P(HW|AZ)  .. from AZ to HW, the -H parameter
  ci  = P_i(C)  .. probability of cross-over at site i, from genetic map
  AZi = P_i(AZ) .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
  HWi = P_i(HW)
  P_{i+1}(AZ) = oAZ * max[(1 - tAZ * ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
  P_{i+1}(HW) = oHW * max[(1 - tHW * ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]


General Options:

--AF-dflt FLOAT

in case allele frequency is not known, use the FLOAT. By default, sites where allele frequency cannot be determined, or is 0, are skipped.

--AF-tag TAG

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

--AF-file FILE

Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF. The file can be compressed with bgzip and indexed with tabix -s1 -b2 -e2. Sites which are not present in the FILE or have different reference or alternate allele will be skipped. Note that such a file can be easily created from a VCF using: 

    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\t%INFO/TAG\n' file.vcf | bgzip -c > freqs.tab.gz

-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

-c, --collapse snps|indels|both|all|some|none

see Common Options

-d, --depth INT,INT,INT

ranges of depth distribution: min, max, and size of the bin

--debug

produce verbose per-site and per-sample output

-e, --exclude EXPRESSION

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

-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.

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