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| BCFTOOLS(1) | 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 2018-04-03 and refers to bcftools git version 1.8.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
• csq .. haplotype aware consequence
caller
• 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
• mpileup .. multi-way pileup producing
genotype likelihoods
• 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
• sort .. sort VCF/BCF files
• 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 "^". The sample order is updated to reflect that given
on the command line. Note that in general tags such as INFO/AC, INFO/AN, etc
are not updated to correspond to the subset samples. 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 sample order is updated to reflect that given
in the input file. 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.
--collapse snps|indels|both|all|some|none
Controls how to match records from the annotation file to
the target VCF. Effective only when -a is a VCF or BCF. See Common
Options for more.
-c, --columns list
Comma-separated list of columns or tags to carry over
from the annotation file (see also -a, --annotations). If the
annotation file is not a VCF/BCF, list describes the columns of the
annotation file and must include CHROM, POS (or, alternatively, FROM and TO),
and optionally REF and ALT. Unused columns which should be ignored can be
indicated by "-".
If the annotation file is a VCF/BCF, only the edited columns/tags must be present and their order does not matter. The columns ID, QUAL, FILTER, INFO and FORMAT can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG", and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG". The imported VCF annotations can be renamed as "DST_TAG:=SRC_TAG" or "FMT/DST_TAG:=FMT/SRC_TAG".
To carry over all INFO annotations, use "INFO". To add all INFO annotations except "TAG", use "^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.
-k, --keep-sites
keep sites wich do not pass -i and -e
expressions instead of discarding them
-m, --mark-sites TAG
annotate sites which are present ("+") or
absent ("-") in the -a file with a new INFO/TAG flag
--no-version
see Common Options
-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 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.
-F, --prior-freqs AN,AC
take advantage of prior knowledge of population allele
frequencies. The workflow looks like this:
# Extract AN,AC values from an existing VCF, such 1000Genomes
bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' 1000Genomes.bcf | bgzip -c > AFs.tab.gz
# If the tags AN,AC are not already present, use the +fill-AN-AC plugin
bcftools +fill-AN-AC 1000Genomes.bcf | bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' | bgzip -c > AFs.tab.gz
tabix -s1 -b2 -e2 AFs.tab.gz
# Create a VCF header description, here we name the tags REF_AN,REF_AC
cat AFs.hdr
##INFO=<ID=REF_AN,Number=1,Type=Integer,Description="Total number of alleles in reference genotypes">
##INFO=<ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele">
# Now before calling, stream the raw mpileup output through `bcftools annotate` to add the frequencies
bcftools mpileup [...] -Ou | bcftools annotate -a AFs.tab.gz -h AFs.hdr -c CHROM,POS,REF,ALT,REF_AN,REF_AC -Ou | bcftools call -mv -F REF_AN,REF_AC [...]
-g, --gvcf INT
output also gVCF blocks of homozygous REF calls. The
parameter INT is the minimum per-sample depth required to include a
site in the non-variant block.
-i, --insert-missed INT
output also sites missed by mpileup but present in -T,
--targets-file.
-M, --keep-masked-ref
output sites where REF allele is N
-V, --skip-variants snps|indels
skip indel/SNP sites
-v, --variants-only
output variant sites only
Consensus/variant calling options:
-c, --consensus-caller
the original samtools/bcftools calling
method (conflicts with -m)
-C, --constrain alleles|trio
alleles
call genotypes given alleles. See also -T,
--targets-file.
trio
call genotypes given the father-mother-child constraint.
See also -s, --samples and -n, --novel-rate.
-m, --multiallelic-caller
alternative modelfor multiallelic and rare-variant
calling designed to overcome known limitations in -c calling model
(conflicts with -c)
-n, --novel-rate float[,...]
likelihood of novel mutation for constrained -C
trio calling. The trio genotype calling maximizes likelihood of a
particular combination of genotypes for father, mother and the child
P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn). By providing
three values, the mutation rate Pn is set explicitly for SNPs, deletions and
insertions, respectively. If two values are given, the first is interpreted as
the mutation rate of SNPs and the second is used to calculate the mutation
rate of indels according to their length as Pn=float*exp(-a-b*len),
where a=22.8689, b=0.2994 for insertions and a=21.9313, b=0.2856 for deletions
[pubmed:23975140]. If only one value is given, the same mutation rate Pn is
used for SNPs and indels.
-p, --pval-threshold float
with -c, accept variant if P(ref|D) <
float.
-P, --prior float
expected substitution rate, or 0 to disable the prior.
Only with -m.
-t, --targets file|chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options
-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 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 concat [OPTIONS] FILE1 FILE2 [...]¶
Concatenate or combine VCF/BCF files. All source files must have the same sample columns appearing in the same order. Can be used, for example, to concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel VCF into one. The input files must be sorted by chr and position. The files must be given in the correct order to produce sorted VCF on output unless the -a, --allow-overlaps option is specified. With the --naive option, the files are concatenated without being recompressed, which is very fast but dangerous if the BCF headers differ.-a, --allow-overlaps
First coordinate of the next file can precede last record
of the current file.
-c, --compact-PS
Do not output PS tag at each site, only at the start of a
new phase set block.
-d, --rm-dups snps|indels|both|all|none
Output duplicate records of specified type present in
multiple files only once. Requires -a, --allow-overlaps.
-D, --remove-duplicates
Alias for -d none
-f, --file-list FILE
Read file names from FILE, one file name per
line.
-l, --ligate
Ligate phased VCFs by matching phase at overlapping
haplotypes
--no-version
see Common Options
-n, --naive
Concatenate VCF or BCF files without recompression. This
is very fast but requires that all files are of the same type (all VCF or all
BCF) and have the same headers. This is because all tags and chromosome names
in the BCF body rely on the implicit order of the contig and tag definitions
in the header. Currently no sanity checks are in place. Dangerous, use with
caution.
-o, --output FILE
see Common Options
-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. By default, the program will apply all ALT variants to the reference fasta to obtain the consensus sequence. Using the --sample (and, optionally, --haplotype) option will apply genotype (haplotype) calls from FORMAT/GT. Note that the program does not act as a primitive variant caller and ignores allelic depth information, such as INFO/AD or FORMAT/AD. For that, consider using the setGT plugin.-c, --chain FILE
write a chain file for liftover
-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For
valid expressions see EXPRESSIONS.
-f, --fasta-ref FILE
reference sequence in fasta format
-H, --haplotype 1|2|R|A|LR|LA|SR|SA
choose which allele from the FORMAT/GT field to use (the
codes are case-insensitive):
1
the first allele
2
the second allele
R
the REF allele (in heterozygous genotypes)
A
the ALT allele (in heterozygous genotypes)
LR, LA
the longer allele. If both have the same length, use the
REF allele (LR), or the ALT allele (LA)
SR, SA
the shorter allele. If both have the same length, use the
REF allele (SR), or the ALT allele (SA)
This option requires *-s*, unless exactly one sample is present in the VCF
-i, --include EXPRESSION
include only sites for which EXPRESSION is true.
For valid expressions see EXPRESSIONS.
-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
--chrom
output chromosome in the first column instead of
CHROM:POS_REF_ALT
--sex FILE
output sex column in the sample file. The FILE format
is
MaleSample M
FemaleSample F
--vcf-ids
output VCF IDs in the second column instead of
CHROM:POS_REF_ALT
gVCF conversion:
--gvcf2vcf
convert gVCF to VCF, expanding REF blocks into sites.
Only sites with FILTER set to "PASS" or "." will be
expanded.
-f, --fasta-ref file
reference sequence in fasta format. Must be indexed with
samtools faidx
HAP/SAMPLE conversion:
--hapsample2vcf prefix or hap-file,sample-file
convert from hap/sample format to VCF. The columns of
.hap file are similar to .gen file above, but there are only two haplotype
columns per sample. Note that the first column of the .hap file is expected to
be in the form "CHR:POS_REF_ALT(_END)?", with the _END being
optional for defining the INFO/END tag when ALT is a symbolic allele, for
example:
.hap ---- 1:111485207_G_A rsID1 111485207 G A 0 1 0 0 1:111494194_C_T rsID2 111494194 C T 0 1 0 0 1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0
--hapsample prefix or hap-file,sample-file
convert from VCF to hap/sample format used by IMPUTE2 and
SHAPEIT. The columns of .hap file begin with ID,RSID,POS,REF,ALT. In order to
prevent strand swaps, the program uses IDs of the form
"CHROM:POS_REF_ALT".
--haploid2diploid
with -h option converts haploid genotypes to
homozygous diploid genotypes. For example, the program will print 0 0
instead of the default 0 -. This is useful for programs which do not
handle haploid genotypes correctly.
--sex FILE
output sex column in the sample file. The FILE format
is
MaleSample M
FemaleSample F
--vcf-ids
output VCF IDs instead of "CHROM:POS_REF_ALT"
IDs
HAP/LEGEND/SAMPLE conversion:
-H, --haplegendsample2vcf prefix or hap-file,legend-file,sample-file
convert from hap/legend/sample format used by IMPUTE2 to
VCF, see also -h, --hapslegendsample below.
-h, --haplegendsample prefix or hap-file,legend-file,sample-file
convert from VCF to hap/legend/sample format used by
IMPUTE2 and SHAPEIT. The columns of .legend file ID,POS,REF,ALT. In order to
prevent strand swaps, the program uses IDs of the form
"CHROM:POS_REF_ALT". The .sample file is quite basic at the moment
with columns for population, group and sex expected to be edited by the user.
For example:
.hap ----- 0 1 0 0 1 0 0 1 0 0 0 1 .legend ------- id position a0 a1 1:111485207_G_A 111485207 G A 1:111494194_C_T 111494194 C T .sample ------- sample population group sex sample1 sample1 sample1 2 sample2 sample2 sample2 2
--haploid2diploid
with -h option converts haploid genotypes to
homozygous diploid genotypes. For example, the program will print 0 0
instead of the default 0 -. This is useful for programs which do not
handle haploid genotypes correctly.
--sex FILE
output sex column in the sample file. The FILE format
is
MaleSample M
FemaleSample F
--vcf-ids
output VCF IDs instead of "CHROM:POS_REF_ALT"
IDs
TSV conversion:
--tsv2vcf file
convert from TSV (tab-separated values) format (such as
generated by 23andMe) to VCF. The input file fields can be tab- or space-
delimited
-c, --columns list
comma-separated list of fields in the input file. In the
current version, the fields CHROM, POS, ID, and AA are expected and can appear
in arbitrary order, columns which should be ignored in the input file can be
indicated by "-". The AA field lists alleles on the forward
reference strand, for example "CC" or "CT" for diploid
genotypes or "C" for haploid genotypes (sex chromosomes). Insertions
and deletions are not supported yet, missing data can be indicated with
"--".
-f, --fasta-ref file
reference sequence in fasta format. Must be indexed with
samtools faidx
-s, --samples LIST
list of sample names. See Common Options
-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 csq [OPTIONS] FILE¶
Haplotype aware consequence predictor which correctly handles combined variants such as MNPs split over multiple VCF records, SNPs separated by an intron (but adjacent in the spliced transcript) or nearby frame-shifting indels which in combination in fact are not frame-shifting.The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the -c option). The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes. See the usage examples below for using the %TBCSQ converter in query for extracting a more human readable form from this bitmask. The contruction of the bitmask limits the number of consequences that can be referenced in the FORMAT/BCSQ tags. By default this is 16, but if more are required, see the --ncsq option.
The program requires on input a VCF/BCF file, the reference genome in fasta format (--fasta-ref) and genomic features in the GFF3 format downloadable from the Ensembl website (--gff-annot), and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3 files are supported.
By default, the input VCF should be phased. If phase is unknown, or only partially known, the --phase option can be used to indicate how to handle unphased data. Alternatively, haplotype aware calling can be turned off with the --local-csq option.
If conflicting (overlapping) variants within one haplotype are detected, a warning will be emitted and predictions will be based on only the first variant in the analysis.
Symbolic alleles are not supported. They will remain unannotated in the output VCF and are ignored for the prediction analysis.
-c, --custom-tag STRING
use this custom tag to store consequences rather than the
default BCSQ tag
-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For
valid expressions see EXPRESSIONS.
-f, --fasta-ref FILE
reference sequence in fasta format (required)
-g, --gff-annot FILE
GFF3 annotation file (required), such as
ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens. An example of a minimal
working GFF file:
# The program looks for "CDS", "exon", "three_prime_UTR" and "five_prime_UTR" lines,
# looks up their parent transcript (determined from the "Parent=transcript:" attribute),
# the gene (determined from the transcript's "Parent=gene:" attribute), and the biotype
# (the most interesting is "protein_coding").
#
# Attributes required for
# gene lines:
# - ID=gene:<gene_id>
# - biotype=<biotype>
# - Name=<gene_name> [optional]
#
# transcript lines:
# - ID=transcript:<transcript_id>
# - Parent=gene:<gene_id>
# - biotype=<biotype>
#
# other lines (CDS, exon, five_prime_UTR, three_prime_UTR):
# - Parent=transcript:<transcript_id>
#
# Supported biotypes:
# - see the function gff_parse_biotype() in bcftools/csq.c
1 ignored_field gene 21 2148 . - . ID=gene:GeneId;biotype=protein_coding;Name=GeneName
1 ignored_field transcript 21 2148 . - . ID=transcript:TranscriptId;Parent=gene:GeneId;biotype=protein_coding
1 ignored_field three_prime_UTR 21 2054 . - . Parent=transcript:TranscriptId
1 ignored_field exon 21 2148 . - . Parent=transcript:TranscriptId
1 ignored_field CDS 21 2148 . - 1 Parent=transcript:TranscriptId
1 ignored_field five_prime_UTR 210 2148 . - . Parent=transcript:TranscriptId
-i, --include EXPRESSION
include only sites for which EXPRESSION is true.
For valid expressions see EXPRESSIONS.
-l, --local-csq
switch off haplotype-aware calling, run localized
predictions considering only one VCF record at a time
-n, --ncsq INT
maximum number of consequences to consider per site. The
INFO/BCSQ column includes all consequences, but only the first INT will
be referenced by the FORMAT/BCSQ fields. The default value is 16 which
corresponds to one integer per diploid sample. Note that increasing the value
leads to increased memory and is rarely necessary.
-o, --output FILE
see Common Options
-O, --output-type b|t|u|z|v
see Common Options. In addition, a custom
tab-delimited plain text output can be printed (t).
-p, --phase a|m|r|R|s
how to handle unphased heterozygous genotypes:
a
take GTs as is, create haplotypes regardless of phase
(0/1 → 0|1)
m
merge all GTs into a single haplotype (0/1 → 1,
1/2 → 1)
r
require phased GTs, throw an error on unphased
heterozygous GTs
R
create non-reference haplotypes if possible (0/1 →
1|1, 1/2 → 1|2)
s
skip unphased heterozygous GTs
-q, --quiet
suppress warning messages
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options
-R, --regions-file FILE
see Common Options
-s, --samples LIST
samples to include or "-" to apply all variants
and ignore samples
-S, --samples-file FILE
see Common Options
-t, --targets LIST
see Common Options
-T, --targets-file FILE
see Common Options
Examples:
# Basic usage
bcftools csq -f hs37d5.fa -g Homo_sapiens.GRCh37.82.gff3.gz in.vcf -Ob -o out.bcf
# Extract the translated haplotype consequences. The following TBCSQ variations
# are recognised:
# %TBCSQ .. print consequences in all haplotypes in separate columns
# %TBCSQ{0} .. print the first haplotype only
# %TBCSQ{1} .. print the second haplotype only
# %TBCSQ{*} .. print a list of unique consquences present in either haplotype
bcftools query -f'[%CHROM\t%POS\t%SAMPLE\t%TBCSQ\n]' out.bcf
Examples of BCSQ annotation:
# Two separate VCF records at positions 2:122106101 and 2:122106102
# change the same codon. This UV-induced C>T dinucleotide mutation
# has been annotated fully at the position 2:122106101 with
# - consequence type
# - gene name
# - ensembl transcript ID
# - coding strand (+ fwd, - rev)
# - amino acid position (in the coding strand orientation)
# - list of corresponding VCF variants
# The annotation at the second position gives the position of the full
# annotation
BCSQ=missense|CLASP1|ENST00000545861|-|1174P>1174L|122106101G>A+122106102G>A
BCSQ=@122106101
# A frame-restoring combination of two frameshift insertions C>CG and T>TGG
BCSQ=@46115084
BCSQ=inframe_insertion|COPZ2|ENST00000006101|-|18AGRGP>18AQAGGP|46115072C>CG+46115084T>TGG
# Stop gained variant
BCSQ=stop_gained|C2orf83|ENST00000264387|-|141W>141*|228476140C>T
# The consequence type of a variant downstream from a stop are prefixed with *
BCSQ=*missense|PER3|ENST00000361923|+|1028M>1028T|7890117T>C
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. The program can operate in two modes. If the -g option is given, the identity of the -s sample from query.vcf.gz is checked against the samples in the -g file. Without the -g option, multi-sample cross-check of samples in query.vcf.gz is performed.-a, --all-sites
output for all sites
-c, --cluster FLOAT,FLOAT
min inter- and max intra-sample error [0.23,-0.3]
The first "min" argument controls the typical error rate in multiplexed
runs ("lanelets") from the same sample. Lanelets with error rate less
than this will always be considered as coming from the same sample.
The second "max" argument is the reverse: lanelets with error rate
greater than the absolute value of this parameter will always be
considered as different samples. When the value is negative, the cutoff
may be heuristically lowered by the clustering engine. If positive, the
value is interpreted as a fixed cutoff.
-g, --genotypes genotypes.vcf.gz
reference genotypes to compare against
-G, --GTs-only INT
use genotypes (GT) instead of genotype likelihoods (PL).
When set to 1, reported discordance is the number of non-matching GTs,
otherwise the number INT is interpreted as phred-scaled likelihood of
unobserved genotypes.
-H, --homs-only
consider only genotypes which are homozygous in both
genotypes and query VCF. This may be useful with low coverage
data.
-p, --plot PREFIX
produce plots
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options
-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.
ERR, error rate
Pairwise error rate calculated as number of differences
divided by the total number of comparisons.
CLUSTER, TH, DOT
In presence of multiple samples, related samples and
outliers can be identified by clustering samples by error rate. A simple
hierarchical clustering based on minimization of standard deviation is used.
This is useful to detect sample swaps, for example in situations where one
sample has been sequenced in multiple runs.
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
-o, --output-file FILE
output file name. If not set, then the index will be
created using the input file name plus a .csi or .tbi
extension
-t, --tbi
generate TBI-format index for VCF files
--threads INT
see Common Options
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
-0 --missing-to-ref
assume genotypes at missing sites are 0/0
-f, --apply-filters LIST
see Common Options
-F, --filter-logic x|+
Set the output record to PASS if any of the inputs is
PASS (x), or apply all filters (+), which is the default.
-g, --gvcf -|FILE
merge gVCF blocks, INFO/END tag is expected. If the
reference fasta file FILE is not given and the dash (-) is
given, unknown reference bases generated at gVCF block splits will be
substituted with N’s. The --gvcf option uses the following
default INFO rules: -i QS:sum,MinDP:min,I16:sum,IDV:max,IMF:max.
-i, --info-rules -|TAG:METHOD[,...]
Rules for merging INFO fields (scalars or vectors) or
- to disable the default rules. METHOD is one of sum,
avg, min, max, join. Default is
DP:sum,DP4:sum if these fields exist in the input files. Fields with no
specified rule will take the value from the first input file. The merged QUAL
value is currently set to the maximum. This behaviour is not user controllable
at the moment.
-l, --file-list FILE
Read file names from FILE, one file name per
line.
-m, --merge snps|indels|both|all|none|id
The option controls what types of multiallelic records
can be created:
-m none .. no new multiallelics, output multiple records instead -m snps .. allow multiallelic SNP records -m indels .. allow multiallelic indel records -m both .. both SNP and indel records can be multiallelic -m all .. SNP records can be merged with indel records -m id .. merge by ID
--no-version
see Common Options
-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 mpileup [OPTIONS] -f ref.fa in.bam [in2.bam [...]]¶
Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files. This is based on the original samtools mpileup command (with the -v or -g options) producing genotype likelihoods in VCF or BCF format, but not the textual pileup output. The mpileup command was transferred to bcftools in order to avoid errors resulting from use of incompatible versions of samtools and bcftools when using in the mpileup+bcftools call pipeline.Individuals are identified from the SM tags in the @RG header lines. Multiple individuals can be pooled in one alignment file, also one individual can be separated into multiple files. If sample identifiers are absent, each input file is regarded as one sample.
Note that there are two orthogonal ways to specify locations in the input file; via -r region and -t positions. The former uses (and requires) an index to do random access while the latter streams through the file contents filtering out the specified regions, requiring no index. The two may be used in conjunction. For example a BED file containing locations of genes in chromosome 20 could be specified using -r 20 -t chr20.bed, meaning that the index is used to find chromosome 20 and then it is filtered for the regions listed in the BED file. Also note that the -r option can be much slower than -t with many regions and can require more memory when multiple regions and many alignment files are processed.
Input options
-6, --illumina1.3+
Assume the quality is in the Illumina 1.3+
encoding.
-A, --count-orphans
Do not skip anomalous read pairs in variant
calling.
-b, --bam-list FILE
List of input alignment files, one file per line
[null]
-B, --no-BAQ
Disable probabilistic realignment for the computation of
base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read
base being misaligned. Applying this option greatly helps to reduce false SNPs
caused by misalignments.
-C, --adjust-MQ INT
Coefficient for downgrading mapping quality for reads
containing excessive mismatches. Given a read with a phred-scaled probability
q of being generated from the mapped posi- tion, the new mapping quality is
about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if
enabled, the recommended value for BWA is 50. [0]
-d, --max-depth INT
At a position, read maximally INT reads per input
file. Note that bcftools has a minimum value of 8000/n where n
is the number of input files given to mpileup. This means the default is
highly likely to be increased. Once above the cross-sample minimum of 8000 the
-d parameter will have an effect. [250]
-E, --redo-BAQ
Recalculate BAQ on the fly, ignore existing BQ tags
-f, --fasta-ref FILE
The faidx-indexed reference file in the FASTA
format. The file can be optionally compressed by bgzip. Reference is
required by default unless the --no-reference option is set
[null]
--no-reference
Do not require the --fasta-ref option.
-G, --read-groups FILE
list of read groups to include or exclude if prefixed
with "^". One read group per line. This file can also be used to
assign new sample names to read groups by giving the new sample name as a
second white-space-separated field, like this: "read_group_id
new_sample_name". If the read group name is not unique, also the bam file
name can be included: "read_group_id file_name sample_name". If all
reads from the alignment file should be treated as a single sample, the
asterisk symbol can be used: "* file_name sample_name". Alignments
without a read group ID can be matched with "?". NOTE: The
meaning of bcftools mpileup -G is the opposite of samtools mpileup
-G.
RG_ID_1
RG_ID_2 SAMPLE_A
RG_ID_3 SAMPLE_A
RG_ID_4 SAMPLE_B
RG_ID_5 FILE_1.bam SAMPLE_A
RG_ID_6 FILE_2.bam SAMPLE_A
* FILE_3.bam SAMPLE_C
? FILE_3.bam SAMPLE_D
-q, -min-MQ INT
Minimum mapping quality for an alignment to be used
[0]
-Q, --min-BQ INT
Minimum base quality for a base to be considered
[13]
-r, --regions CHR|CHR:POS|CHR:FROM-TO|CHR:FROM-[,...]
Only generate mpileup output in given regions. Requires
the alignment files to be indexed. If used in conjunction with -l then
considers the intersection; see Common Options
-R, --regions-file FILE
As for -r, --regions, but regions read from FILE;
see Common Options
--ignore-RG
Ignore RG tags. Treat all reads in one alignment file as
one sample.
--rf, --incl-flags STR|INT
Required flags: skip reads with mask bits unset
[null]
--ff, --excl-flags STR|INT
Filter flags: skip reads with mask bits set
[UNMAP,SECONDARY,QCFAIL,DUP]
-s, --samples LIST
list of sample names. See Common Options
-S, --samples-file FILE
file of sample names to include or exclude if prefixed
with "^". One sample per line. This file can also be used to rename
samples by giving the new sample name as a second white-space-separated
column, like this: "old_name new_name". If a sample name contains
spaces, the spaces can be escaped using the backslash character, for example
"Not\ a\ good\ sample\ name".
-t, --targets LIST
see Common Options
-T, --targets-file FILE
see Common Options
-x, --ignore-overlaps
Disable read-pair overlap detection.
Output options
-a, --annotate LIST
Comma-separated list of FORMAT and INFO tags to output.
(case-insensitive, the "FORMAT/" prefix is optional, and use
"?" to list available annotations on the command line) [null]:
*FORMAT/AD* .. Allelic depth (Number=R,Type=Integer) *FORMAT/ADF* .. Allelic depths on the forward strand (Number=R,Type=Integer) *FORMAT/ADR* .. Allelic depths on the reverse strand (Number=R,Type=Integer) *FORMAT/DP* .. Number of high-quality bases (Number=1,Type=Integer) *FORMAT/SP* .. Phred-scaled strand bias P-value (Number=1,Type=Integer)
*INFO/AD* .. Total allelic depth (Number=R,Type=Integer) *INFO/ADF* .. Total allelic depths on the forward strand (Number=R,Type=Integer) *INFO/ADR* .. Total allelic depths on the reverse strand (Number=R,Type=Integer)
*FORMAT/DV* .. Deprecated in favor of FORMAT/AD;
Number of high-quality non-reference bases, (Number=1,Type=Integer)
*FORMAT/DP4* .. Deprecated in favor of FORMAT/ADF and FORMAT/ADR;
Number of high-quality ref-forward, ref-reverse,
alt-forward and alt-reverse bases (Number=4,Type=Integer)
*FORMAT/DPR* .. Deprecated in favor of FORMAT/AD;
Number of high-quality bases for each observed allele (Number=R,Type=Integer)
*INFO/DPR* .. Deprecated in favor of INFO/AD;
Number of high-quality bases for each observed allele (Number=R,Type=Integer)
-g, --gvcf INT[,...]
output gVCF blocks of homozygous REF calls, with depth
(DP) ranges specified by the list of integers. For example, passing
5,15 will group sites into two types of gVCF blocks, the first with
minimum per-sample DP from the interval [5,15) and the latter with minimum
depth 15 or more. In this example, sites with minimum per-sample depth less
than 5 will be printed as separate records, outside of gVCF blocks.
--no-version
see Common Options
-o, --output FILE
Write output to FILE, rather than the default of
standard output. (The same short option is used for both --open-prob
and --output. If -o's argument contains any non-digit characters
other than a leading + or - sign, it is interpreted as --output.
Usually the filename extension will take care of this, but to write to an
entirely numeric filename use -o ./123 or --output 123.)
-O, --output-type b|u|z|v
see Common Options
--threads INT
see Common Options
Options for SNP/INDEL genotype likelihood computation
-e, --ext-prob INT
Phred-scaled gap extension sequencing error probability.
Reducing INT leads to longer indels [20]
-F, --gap-frac FLOAT
Minimum fraction of gapped reads [0.002]
-h, --tandem-qual INT
Coefficient for modeling homopolymer errors. Given an
l-long homopolymer run, the sequencing error of an indel of size s is
modeled as INT*s/l [100]
-I, --skip-indels
Do not perform INDEL calling
-L, --max-idepth INT
Skip INDEL calling if the average per-sample depth is
above INT [250]
-m, --min-ireads INT
Minimum number gapped reads for indel candidates
INT [1]
-o, --open-prob INT
Phred-scaled gap open sequencing error probability.
Reducing INT leads to more indel calls. (The same short option is used
for both --open-prob and --output. When -o’s argument
contains only an optional + or - sign followed by the digits 0 to 9, it is
interpreted as --open-prob.) [40]
-p, --per-sample-mF
Apply -m and -F thresholds per sample to
increase sensitivity of calling. By default both options are applied to reads
pooled from all samples.
-P, --platforms STR
Comma-delimited list of platforms (determined by
@RG-PL) from which indel candidates are obtained. It is recommended to
collect indel candidates from sequencing technologies that have low indel
error rate such as ILLUMINA [all]
Examples:
Call SNPs and short INDELs, then mark low quality sites and sites with the read depth exceeding a limit. (The read depth should be adjusted to about twice the average read depth as higher read depths usually indicate problematic regions which are often enriched for artefacts.) One may consider to add -C50 to mpileup if mapping quality is overestimated for reads containing excessive mismatches. Applying this option usually helps for BWA-backtrack alignments, but may not other aligners.
bcftools mpileup -Ou -f ref.fa aln.bam | \
bcftools call -Ou -mv | \
bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > var.flt.vcf
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 multiple times, output only the
first instance, see --collapse in Common Options.
-D, --remove-duplicates
If a record is present in multiple files, output only the
first instance. Alias for -d none, deprecated.
-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]¶
A common framework for various utilities. The plugins can be used the same way as normal commands only their name is prefixed with "+". Most plugins accept two types of parameters: general options shared by all plugins followed by a separator, and a list of plugin-specific options. There are some exceptions to this rule, some plugins do not accept the common options and implement their own parameters. Therefore please pay attention to the usage examples that each plugin comes with.VCF input options:
-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For
valid expressions see EXPRESSIONS.
-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.
-v, --verbose
print debugging information to debug plugin failure
-V, --version
print version string and exit
List of plugins coming with the distribution:
GTisec
count genotype intersections across all possible sample
subsets in a vcf file
GTsubset
output only sites where the requested samples all
exclusively share a genotype
ad-bias
find positions with wildly varying ALT allele frequency
(Fisher test on FMT/AD)
af-dist
collect AF deviation stats and GT probability
distribution given AF and assuming HWE
check-ploidy
check if ploidy of samples is consistent for all
sites
check-sparsity
print samples without genotypes in a region or
chromosome
color-chrs
color shared chromosomal segments, requires trio VCF with
phased GTs
counts
a minimal plugin which counts number of SNPs, Indels, and
total number of sites.
dosage
print genotype dosage. By default the plugin searches for
PL, GL and GT, in that order.
fill-AN-AC
fill INFO fields AN and AC.
fill-from-fasta
fill INFO or REF field based on values in a fasta
file
fill-tags
set INFO tags AF, AC, AC_Hemi, AC_Hom, AC_Het, AN, HWE,
MAF, NS
fix-ploidy
sets correct ploidy
fixref
determine and fix strand orientation
frameshifts
annotate frameshift indels
guess-ploidy
determine sample sex by checking genotype likelihoods
(GL,PL) or genotypes (GT) in the non-PAR region of chrX.
impute-info
add imputation information metrics to the INFO field
based on selected FORMAT tags
isecGT
compare two files and set non-identical genotypes to
missing
mendelian
count Mendelian consistent / inconsistent
genotypes.
missing2ref
sets missing genotypes ("./.") to ref allele
("0/0" or "0|0")
prune
prune sites by missingness or linkage
disequilibrium
setGT
general tool to set genotypes according to rules
requested by the user
tag2tag
convert between similar tags, such as GL and GP
trio-switch-rate
calculate phase switch rate in trio samples, children
samples must have phased GTs.
Examples:
# List options common to all plugins bcftools plugin # List available plugins bcftools plugin -l # Run a plugin bcftools plugin counts in.vcf # Run a plugin using the abbreviated "+" notation bcftools +counts in.vcf # The input VCF can be streamed just like in other commands cat in.vcf | bcftools +counts # Print usage information of plugin "dosage" bcftools +dosage -h # Replace missing genotypes with 0/0 bcftools +missing2ref in.vcf # Replace missing genotypes with 0|0 bcftools +missing2ref in.vcf -- -p
Plugins troubleshooting:
Things to check if your plugin does not show up in the bcftools plugin -l output:
•Run with the -v option for verbose output:
bcftools plugin -lv
•Does the environment variable BCFTOOLS_PLUGINS
include the correct path?
Plugins API:
// Short description used by 'bcftools plugin -l' const char *about(void); // Longer description used by 'bcftools +name -h' const char *usage(void); // Called once at startup, allows initialization of local variables. // Return 1 to suppress normal VCF/BCF header output, -1 on critical // errors, 0 otherwise. int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr); // Called for each VCF record, return NULL to suppress the output bcf1_t *process(bcf1_t *rec); // Called after all lines have been processed to clean up void destroy(void);
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, BND, OTHER)
%MASK Indicates presence of the site in other files (with multiple files)
%TAG{INT} Curly brackets to subscript vectors (0-based)
%FIRST_ALT Alias for %ALT{0}
[] Format fields must be enclosed in brackets to loop over all samples
%GT Genotype (e.g. 0/1)
%TBCSQ Translated FORMAT/BCSQ. See the csq command above for explanation and examples.
%TGT Translated genotype (e.g. C/A)
%IUPACGT Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
%LINE Prints the whole line
%SAMPLE Sample name
%POS0 POS in 0-based coordinates
%END End position of the REF allele
%END0 End position of the REF allele in 0-based cordinates
\n new line
\t tab character
Everything else is printed verbatim.
Examples:
# Print chromosome, position, ref allele and the first alternate allele
bcftools query -f '%CHROM %POS %REF %ALT{0}\n' file.vcf.gz
# Similar to above, but use tabs instead of spaces, add sample name and genotype bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz
# Print FORMAT/GT fields followed by FORMAT/GT fields bcftools query -f 'GQ:[ %GQ] \t GT:[ %GT]\n' file.vcf
# Make a BED file: chr, pos (0-based), end pos (1-based), id bcftools query -f'%CHROM\t%POS0\t%END\t%ID\n' file.bcf
# Print only samples with alternate (non-reference) genotypes bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf
# Print all samples at sites with at least one alternate genotype bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]'
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
-b, --buffer-size INT[,INT]
when the entire many-sample file cannot fit into memory,
a sliding buffer approach can be used. The first value is the number of sites
to keep in memory. If negative, it is interpreted as the maximum memory to
use, in MB. The second, optional, value sets the number of overlapping sites.
The default overlap is set to roughly 1% of the buffer size.
-e, --estimate-AF FILE
estimate the allele frequency by recalculating INFO/AC
and INFO/AN on the fly, using the specified TAG which can be either
FORMAT/GT ("GT") or FORMAT/PL ("PL"). If TAG is not
given, "GT" is assumed. Either all samples ("-") or
samples listed in FILE will be included. For example, use
"PL,-" to estimate AF from FORMAT/PL of all samples. If neither
-e nor the other --AF-... options are given, the allele
frequency is estimated from AC and AN counts which are already present in the
INFO field.
--exclude EXPRESSION
exclude sites for which EXPRESSION is true. For
valid expressions see EXPRESSIONS.
-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.
--include EXPRESSION
include only sites for which EXPRESSION is true.
For valid expressions see EXPRESSIONS.
-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. In combination with
--genetic-map, the --rec-rate parameter is interpreted
differently, as FLOAT-fold increase of transition probabilities, which
allows the model to become more sensitive yet still account for recombination
hotspots. Note that also the range of the values is therefore different in
both cases: normally the parameter will be in the range (1e-3,1e-9) but with
--genetic-map it will be in the range (10,1000).
-o, --output FILE
Write output to the FILE, by default the output is
printed on stdout
-O, --output-type s|r[z]
Generate per-site output (s) or per-region output
(r). By default both types are printed and the output is uncompressed.
Add z for a compressed output.
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
see Common Options
-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
HMM Options:
-a, --hw-to-az FLOAT
P(AZ|HW) transition probability from AZ (autozygous) to
HW (Hardy-Weinberg) state
-H, --az-to-hw FLOAT
P(HW|AZ) transition probability from HW to AZ state
-V, --viterbi-training FLOAT
estimate HMM parameters using Baum-Welch algorithm, using
the convergence threshold FLOAT, e.g. 1e-10 (experimental)
bcftools sort [OPTIONS] file.bcf¶
-m, --max-mem FLOAT[kMG]Maximum memory to use. Approximate, affects the number of
temporary files written to the disk. Note that if the command fails at this
step because of too many open files, your system limit on the number of open
files ("ulimit") may need to be increased.
-o, --output FILE
see Common Options
-O, --output-type b|u|z|v
see Common Options
-T, --temp-dir DIR
Use this directory to store temporary files
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. When one VCF file is specified on the command line, then stats by non-reference allele frequency, depth distribution, stats by quality and per-sample counts, singleton stats, etc. are printed. When two VCF files are given, then stats such as concordance (Genotype concordance by non-reference allele frequency, Genotype concordance by sample, Non-Reference Discordance) and correlation are also printed. Per-site discordance (PSD) is also printed in --verbose mode.--af-bins LIST|FILE
comma separated list of allele frequency bins (e.g.
0.1,0.5,1) or a file listing the allele frequency bins one per line (e.g.
0.1\n0.5\n1)
--af-tag TAG
allele frequency INFO tag to use for binning. By default
the allele frequency is estimated from AC/AN, if available, or directly from
the genotypes (GT) if not.
-1, --1st-allele-only
consider only the 1st alternate allele at multiallelic
sites
-c, --collapse snps|indels|both|all|some|none
see Common Options
-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|ref|bnd|other
comma-separated list of variant types to exclude. Site is
excluded if any of the ALT alleles is of the type requested. Types are
determined by comparing the REF and ALT alleles in the VCF record not INFO
tags like INFO/INDEL or INFO/VT. Use --exclude to exclude based on INFO
tags.
-x, --private
print sites where only the subset samples carry an
non-reference allele. Requires --samples or
--samples-file.
-X, --exclude-private
exclude sites where only the subset samples carry an
non-reference allele
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 most of the commands.Valid expressions may contain:
•numerical constants, string constants, file names
1, 1.0, 1e-4 "String" @file_name
•arithmetic operators
+,*,-,/
•comparison operators
== (same as =), >, >=, <=, <, !=
•regex operators "~" and its negation
"!~". The expressions are case sensitive unless "/i" is
added.
INFO/HAYSTACK ~ "needle" INFO/HAYSTACK ~ "NEEDless/i"
•parentheses
(, )
•logical operators
&& (same as &), ||, |
•INFO tags, FORMAT tags, column names
INFO/DP or DP FORMAT/DV, FMT/DV, or DV FILTER, QUAL, ID, POS, REF, ALT[0]
•1 (or 0) to test the presence (or absence) of a
flag
FlagA=1 && FlagB=0
•"." to test missing values
DP=".", DP!=".", ALT="."
•missing genotypes can be matched regardless of
phase and ploidy (".|.", "./.", ".") using these
expressions
GT~"\.", GT!~"\."
•missing genotypes can be matched including the
phase and ploidy (".|.", "./.", ".") using these
expressions
GT=".|.", GT="./.", GT="."
•sample genotype: reference (haploid or diploid),
alternate (hom or het, haploid or diploid), missing genotype, homozygous,
heterozygous, haploid, ref-ref hom, alt-alt hom, ref-alt het, alt-alt het,
haploid ref, haploid alt (case-insensitive)
GT="ref" GT="alt" GT="mis" GT="hom" GT="het" GT="hap" GT="RR" GT="AA" GT="RA" or GT="AR" GT="Aa" or GT="aA" GT="R" GT="A"
•TYPE for variant type in REF,ALT columns
(indel,snp,mnp,ref,bnd,other). Use the regex operator "\~" to
require at least one allele of the given type or the equal sign "="
to require that all alleles are of the given type. Compare
TYPE="snp" TYPE~"snp" TYPE!="snp" TYPE!~"snp"
•array subscripts (0-based), "*" for any
element, "-" to indicate a range. Note that for querying FORMAT
vectors, the colon ":" can be used to select a sample and an element
of the vector, as shown in the examples below
INFO/AF[0] > 0.3 .. first AF value bigger than 0.3 FORMAT/AD[0:0] > 30 .. first AD value of the first sample bigger than 30 FORMAT/AD[0:1] .. first sample, second AD value FORMAT/AD[1:0] .. second sample, first AD value DP4[*] == 0 .. any DP4 value FORMAT/DP[0] > 30 .. DP of the first sample bigger than 30 FORMAT/DP[1-3] > 10 .. samples 2-4 FORMAT/DP[1-] < 7 .. all samples but the first FORMAT/DP[0,2-4] > 20 .. samples 1, 3-5 FORMAT/AD[0:1] .. first sample, second AD field FORMAT/AD[0:*], AD[0:] or AD[0] .. first sample, any AD field FORMAT/AD[*:1] or AD[:1] .. any sample, second AD field (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3 CSQ[*] ~ "missense_variant.*deleterious"
•function on FORMAT tags (over samples) and INFO
tags (over vector fields)
MAX, MIN, AVG, SUM, STRLEN, ABS, COUNT
•variables calculated on the fly if not present:
number of alternate alleles; number of samples; count of alternate alleles;
minor allele count (similar to AC but is always smaller than 0.5); frequency
of alternate alleles (AF=AC/AN); frequency of minor alleles (MAF=MAC/AN);
number of alleles in called genotypes; number of samples with missing
genotype; fraction of samples with missing genotype
N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN, N_MISSING, F_MISSING
•custom perl filtering. Note that this command is
not compiled in by default, see the section Optional Compilation with
Perl in the INSTALL file for help and misc/demo-flt.pl for a working
example. The demo defined the perl subroutine "severity" which can
be invoked from the command line as follows:
perl:path/to/script.pl; perl.severity(INFO/CSQ) > 3
Notes:
•String comparisons and regular expressions are
case-insensitive
•Variables and function names are
case-insensitive, but not tag names. For example, "qual" can be used
instead of "QUAL", "strlen()" instead of
"STRLEN()" , but not "dp" instead of "DP".
•When querying multiple values, all elements are
tested and the OR logic is used on the result. For example, when querying
"TAG=1,2,3,4", it will be evaluated as follows:
-i 'TAG[*]=1' .. true, the record will be printed -i 'TAG[*]!=1' .. true -e 'TAG[*]=1' .. false, the record will be discarded -e 'TAG[*]!=1' .. false -i 'TAG[0]=1' .. true -i 'TAG[0]!=1' .. false -e 'TAG[0]=1' .. false -e 'TAG[0]!=1' .. true
Examples:
MIN(DV)>5
MIN(DV/DP)>0.3
MIN(DP)>10 & MIN(DV)>3
FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
QUAL>10 | FMT/GQ>10 .. true for sites with QUAL>10 or a sample with GQ>10, but selects only samples with GQ>10
QUAL>10 || FMT/GQ>10 .. true for sites with QUAL>10 or a sample with GQ>10, plus selects all samples at such sites
TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
COUNT(GT="hom")=0
MIN(DP)>35 && AVG(GQ)>50
ID=@file .. selects lines with ID present in the file
ID!=@~/file .. skip lines with ID present in the ~/file
MAF[0]<0.05 .. select rare variants at 5% cutoff
POS>=100 .. restrict your range query, e.g. 20:100-200 to strictly sites with POS in that range.
Shell expansion:
Note that expressions must often be quoted because some characters have special meaning in the shell. An example of expression enclosed in single quotes which cause that the whole expression is passed to the program as intended:
bcftools view -i '%ID!="." & MAF[0]<0.01'
Please refer to the documentation of your shell for details.
SCRIPTS AND OPTIONS¶
plot-vcfstats [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 DIR
The output directory. This directory will be created if
it does not exist.
-P, --no-PDF
Skip the PDF creation step.
-r, --rasterize
Rasterize PDF images for faster rendering.
-s, --sample-names
Use sample names for xticks rather than numeric
IDs.
-t, --title STRING
Identify files by these titles in plots. The option can
be given multiple times, for each ID in the 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/bcftoolsAUTHORS¶
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/bcftoolsSamtools 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.| 2018-04-03 |