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.VERSION
This manual page was last updated 2022-08-18 and refers to bcftools git version 1.16.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
•head .. view VCF/BCF file
headers
•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.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.
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
some
all
snps
indels
both
id
only records with identical REF and ALT
alleles are compatible
only records where some subset of ALT alleles
match are compatible
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.
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.
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.
abbreviation of "-c
indels -c snps"
only records with identical ID column are
compatible. Supported by bcftools merge only.
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.
Do not append version and command line
information to the output VCF header.
When output consists of a single stream, write
it to FILE rather than to standard output, where it is written by
default. The file type is determined automatically from the file name suffix
and in case a conflicting -O option is given, the file name suffix
takes precedence.
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. The compression level of the
compressed formats ( b and z) can be set by by appending a
number between 0-9.
Comma-separated list of regions, see also
-R, --regions-file. Overlapping records are matched even when the
starting coordinate is outside of the region, unlike the -t/-T options
where only the POS coordinate is checked. Note that -r cannot be used
in combination with -R.
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 can contain either positions (two-column format) or
intervals (three-column format): CHROM, POS, and, optionally, END, where
positions are 1-based and inclusive. The columns of the tab-delimited BED file
are also CHROM, POS and END (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.
This option controls how overlapping records
are determined: set to pos or 0 if the VCF record has to have
POS inside a region (this corresponds to the default behavior of
-t/-T); set to record or 1 if also overlapping records
with POS outside a region should be included (this is the default behavior of
-r/-R, and includes indels with POS at the end of a region, which are
technically outside the region); or set to variant or 2 to
include only true overlapping variation (compare the full VCF representation
"TA>T-" vs the true sequence variation "A>-").
Comma-separated list of samples to include or
exclude if prefixed with "^." (Note that when multiple samples are
to be excluded, the "^" prefix is still present only once, e.g.
"^SAMPLE1,SAMPLE2".) 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
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"), for
example:
sample1 1
sample2 2
sample3 2
sample1 M
sample2 F
sample3 F
ignored_column daughterA fatherA motherA 2
ignored_column sonB fatherB motherB 1
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 -t/-T and -r/-R is that
-r/-R checks for proper overlaps and considers both POS and the end
position of an indel, while -t/-T considers the POS coordinate only (by
default; see also --regions-overlap and --targets-overlap). Note
that -t cannot be used in combination with -T.
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 indexed. 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
Same as --regions-overlap but for
-t/-T.
Use multithreading with INT worker
threads. The option is currently used only for the compression of the output
stream, only when --output-type is b or z. Default:
0.
bcftools annotate [OPTIONS] FILE
Add or remove annotations.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. If the END
coordinate is present in the annotation file and given on command line as
"-c ~INFO/END", then VCF records will be matched also by the
INFO/END coordinate. If ID is present in the annotation file and given as
"-c ~ID", then VCF records will be matched also by the ID column.
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.
Missing values can be added by providing "." in place of actual value
and using the missing value modifier with -c, such as ".TAG".
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
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.
By default, existing tags are overwritten unless the source value is a missing
value (i.e. "."). If also missing values should be carried over (and
overwrite existing tags), use ".TAG" instead of "TAG". To
add annotations without overwriting existing values (that is, to add tags that
are absent or to add values to existing tags with missing values), use
"+TAG" instead of "TAG". These can be combined, for
example ".+TAG" can be used to add TAG even if the source value is
missing but only if TAG does not exist in the target file; existing tags will
not be overwritten. 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". To match the record also by ID or INFO/END,
in addition to REF and ALT, use "~ID" or "~INFO/END". If
position needs to be replaced, mark the column with the new position as
"~POS".
If the annotation file is not a VCF/BCF, all new annotations must be defined via
-h, --header-lines.
See also the -l, --merge-logic option.
Read the list of columns from a file (normally
given via the -c, --columns option). "-" to skip a column of
the annotation file. One column name per row, an additional space- or
tab-separated field can be present to indicate the merge logic (normally given
via the -l, --merge-logic option). This is useful when many annotations
are added at once.
exclude sites for which EXPRESSION is
true. For valid expressions see EXPRESSIONS.
continue even when parsing errors, such as
undefined tags, are encountered. Note this can be an unsafe operation and can
result in corrupted BCF files. If this option is used, make sure to sanity
check the result thoroughly.
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">
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
include only sites for which EXPRESSION
is true. For valid expressions see EXPRESSIONS.
keep sites which do not pass -i and
-e expressions instead of discarding them
When multiple regions overlap a single record,
this option defines how to treat multiple annotation values when setting
tag in the destination file: use the first encountered value ignoring
the rest ( first); append allowing duplicates (append); append
even if the appended value is missing, i.e. is a dot ( append-missing);
append discarding duplicate values ( unique); sum the values (
sum, numeric fields only); average the values ( avg); use the
minimum value ( min) or the maximum ( max). + Note that this
option is intended for use with BED or TAB-delimited annotation files only.
Moreover, it is effective only when either REF and ALT or
BEG and END --columns are present . + Multiple rules can
be given either as a comma-separated list or giving the option multiple times.
This is an experimental feature.
annotate sites which are present
("+") or absent ("-") in the -a file with a new
INFO/TAG flag
minimum overlap required as a fraction of the
variant in the annotation -a file (ANN), in the target VCF file
( :VCF), or both for reciprocal overlap (ANN:VCF). By default
overlaps of arbitrary length are sufficient. The option can be used only with
the tab-delimited annotation -a file and with BEG and END
columns present.
see Common Options
see Common Options
see Common Options
Controls how to match records from the
annotation file to the target VCF. Effective only when -a is a VCF or
BCF. The option replaces the former uninuitive --collapse. See
Common Options for more.
see Common Options
see Common Options
see Common Options
rename annotations according to the map in
file, with "old_name new_name\n" pairs separated by
whitespaces, each on a separate line. The old name must be prefixed with the
annotation type: INFO, FORMAT, or FILTER.
rename chromosomes according to the map in
file, with "old_name new_name\n" pairs separated by
whitespaces, each on a separate line.
subset of samples to annotate, see also
Common Options
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.
use this option to keep memory requirements
low with very large annotation files. Note, however, that this comes at a
cost, only single overlapping intervals are considered in this mode. This was
the default mode until the commit af6f0c9 (Feb 24 2019).
see Common Options
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".
# 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 input.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
# Transfer the INFO/END tag, matching by POS,REF,ALT and ID. This example assumes
# that INFO/END is already present in the VCF header.
bcftools annotate -a annots.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END input.vcf
# For more examples see http://samtools.github.io/bcftools/howtos/annotate.html
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 <http://github.com/samtools/htslib>, but will be added back on popular demand. The original calling model can be invoked with the -c option.File format options:
--no-versionsee Common Options
see Common Options
see Common Options
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 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
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
Input/output options:
-A, --keep-altsoutput all alternate alleles present in the
alignments even if they do not appear in any of the genotypes
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. Prefixed with
"^" indicates a request for tag removal of auxiliary tags useful
only for calling.
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-tags plugin
bcftools +fill-tags 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 [...]
by default, all samples are assumed to come
from a single population. This option allows to group samples into populations
and apply the HWE assumption within but not across the populations.
FILE is a tab-delimited text file with sample names in the first column
and group names in the second column. If - is given instead, no HWE
assumption is made at all and single-sample calling is performed. (Note that
in low coverage data this inflates the rate of false positives.) The -G
option requires the presence of per-sample FORMAT/QS or FORMAT/AD tag
generated with bcftools mpileup -a QS (or -a AD).
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.
output also sites missed by mpileup but
present in -T, --targets-file.
output sites where REF allele is N
skip indel/SNP sites
output variant sites only
Consensus/variant calling options:
-c, --consensus-callerthe original samtools/bcftools
calling method (conflicts with -m)
call genotypes given alleles. See also -T,
--targets-file.
call genotypes given the father-mother-child
constraint. See also -s, --samples and -n, --novel-rate.
alternative model for multiallelic and
rare-variant calling designed to overcome known limitations in -c
calling model (conflicts with -c)
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.
with -c, accept variant if P(ref|D)
< float.
expected substitution rate, or 0 to disable
the prior. Only with -m.
see Common Options
haploid output for male samples (requires PED
file with -s)
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 stringoptional control sample name. If given,
pairwise calling is performed and the -P option can be used
read allele frequencies from a tab-delimited
file with the columns CHR,POS,REF,ALT,AF
output directory
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.
see Common Options
see Common Options
see Common Options
query sample name
see Common Options
see Common Options
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.
relative contribution from BAF
expected BAF deviation in query and control,
i.e. the noise observed in the data.
uniform error probability
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).
reduce LRR noise by applying moving average
given this window size
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
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.
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..First coordinate of the next file can precede
last record of the current file.
Do not output PS tag at each site, only at the
start of a new phase set block.
Output duplicate records of specified type
present in multiple files only once. Note that records duplicate within one
file are not removed with this option, for that use bcftools norm -d
instead.
In other words, the default behavior of the program is similar to unix
"cat" in that when two files contain a record with the same
position, that position will appear twice on output. With -d, every
line that finds a matching record in another file will be printed only once.
Requires -a, --allow-overlaps.
Alias for -d exact
Read file names from FILE, one file
name per line.
Ligate phased VCFs by matching phase at
overlapping haplotypes. Note that the option is intended for VCFs with perfect
overlap, sites in overlapping regions present in one but missing in the other
are dropped.
Keep all sites and ligate even non-overlapping
chunks and chunks with imperfect overlap
Drop sites in imperfect overlaps
see Common Options
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 order of the contig and tag
definitions in the header. A header check compatibility is performed and the
program throws an error if it is not safe to use the option.
Same as --naive, but header compatibility is
not checked. Dangerous, use with caution.
see Common Options
see Common Options
Break phase set if phasing quality is lower
than INT
see Common Options. Requires -a,
--allow-overlaps.
see Common Options. Requires -a,
--allow-overlaps.
see Common Options
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.replace positions absent from VCF with
CHAR
write a chain file for liftover
exclude sites for which EXPRESSION is
true. For valid expressions see EXPRESSIONS.
reference sequence in fasta format
choose which allele from the FORMAT/GT field
to use (the codes are case-insensitive):
1
2
R
A
I
LR, LA
SR, SA
1pIu, 2pIu
the first allele, regardless of phasing
the second allele, regardless of phasing
the REF allele (in heterozygous
genotypes)
the ALT allele (in heterozygous
genotypes)
IUPAC code for all genotypes
the longer allele. If both have the same
length, use the REF allele (LR), or the ALT allele (LA)
the shorter allele. If both have the same
length, use the REF allele (SR), or the ALT allele (SA)
first/second allele for phased genotypes and
IUPAC code for unphased genotypes
This option requires *-s*, unless exactly one sample is present in the VCF
include only sites for which EXPRESSION
is true. For valid expressions see EXPRESSIONS.
output variants in the form of IUPAC ambiguity
codes
instead of removing sequence, insert CHAR for
deletions
highlight inserted sequence in uppercase (uc)
or lowercase (lc), leaving the rest of the sequence as is
highlight substitutions in uppercase (uc) or
lowercase (lc), leaving the rest of the sequence as is
BED file or TAB file with regions to be
replaced with N (the default) or as specified by the next --mask-with
option. See discussion of --regions-file in Common Options for
file format details.
replace sequence from --mask with CHAR,
skipping overlapping variants, or change to lowercase (lc) or uppercase
(uc)
instead of skipping the missing genotypes,
output the character CHAR (e.g. "?")
write output to a file
apply variants of the given sample
# 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
# For more examples see http://samtools.github.io/bcftools/howtos/consensus-sequence.html
bcftools convert [OPTIONS] FILE
VCF input options:
-e, --exclude EXPRESSIONexclude sites for which EXPRESSION is
true. For valid expressions see EXPRESSIONS.
include only sites for which EXPRESSION
is true. For valid expressions see EXPRESSIONS.
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
VCF output options:
--no-versionsee Common Options
see Common Options
see Common Options
see Common Options
GEN/SAMPLE conversion:
-G, --gensample2vcf prefix or gen-file,sample-fileconvert IMPUTE2 output to VCF. One of the ID
columns ("SNP ID" or "rsID" in
<https://www.cog-genomics.org/plink/2.0/formats#gen>) must be of the
form "CHROM:POS_REF_ALT" to detect possible strand swaps.
When the --vcf-ids option is given, the other column (autodetected) is
used to fill the ID column of the VCF.
See also -g and --3N6 options.
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". When the --vcf-ids option is given, the
second column is set to match the ID column of the VCF.
See also -G and --3N6 options.
The file .gen and .sample file format are:
.gen (with --3N6 --vcf-ids) --------------------------- chr1 1:111485207_G_A rsID1 111485207 G A 0 1 0 0 1 0 chr1 1:111494194_C_T rsID2 111494194 C T 0 1 0 0 0 1 .gen (with --vcf-ids) --------------------------- 1:111485207_G_A rsID1 111485207 G A 0 1 0 0 1 0 1:111494194_C_T rsID2 111494194 C T 0 1 0 0 0 1 .gen (the default) ------------------------------ 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
Expect/Create files in the 3*N+6 column
format. This is the new .gen file format with the first column containing the
chromosome name, see
<https://www.cog-genomics.org/plink/2.0/formats#gen>
tag to take values for .gen file:
GT,PL,GL,GP
output sex column in the sample file. The FILE
format is
MaleSample M
FemaleSample F
output VCF IDs in the second column instead of
CHROM:POS_REF_ALT
gVCF conversion:
--gvcf2vcfconvert gVCF to VCF, expanding REF blocks into
sites. Note that the -i and -e options work differently with
this switch. In this situation the filtering expressions define which sites
should be expanded and which sites should be left unmodified, but all sites
are printed on output. In order to drop sites, stream first through
bcftools view.
reference sequence in fasta format. Must be
indexed with samtools faidx
HAP/SAMPLE conversion:
--hapsample2vcf prefix or hap-file,sample-fileconvert 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 or the second 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 (with --vcf-ids) --------------------- 1:111485207_G_A rsID1 111485207 G A 0 1 0 0 1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0 .hap (the default) ------------------ 1 1:111485207_G_A 111485207 G A 0 1 0 0 1 1:111495231_A_<DEL>_111495784 111495231 A <DEL> 0 0 1 0
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".
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.
output sex column in the sample file. The FILE
format is
MaleSample M
FemaleSample F
the second column of the .hap file holds the
VCF ids, the first column is of the form "CHR:POS_REF_ALT[_END]".
Without the option, the format follows
<https://www.cog-genomics.org/plink/2.0/formats#haps> with ids (the
second column) of the form "CHR:POS_REF_ALT[_END]"
HAP/LEGEND/SAMPLE conversion:
-H, --haplegendsample2vcf prefix or hap-file,legend-file, sample-fileconvert from hap/legend/sample format used by
IMPUTE2 to VCF. See also -h, --hapslegendsample below.
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
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.
output sex column in the sample file. The FILE
format is
MaleSample M
FemaleSample F
output VCF IDs instead of
"CHROM:POS_REF_ALT". Note that this option can be used with
--haplegendsample but not with --haplegendsample2vcf.
TSV conversion:
--tsv2vcf fileconvert from TSV (tab-separated values) format
(such as generated by 23andMe) to VCF. The input file fields can be tab- or
space- delimited
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 "--".
reference sequence in fasta format. Must be
indexed with samtools faidx
list of sample names. See Common
Options
file of sample names. See Common
Options
# 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.use this custom tag to store consequences
rather than the default BCSQ tag
abbreviate protein-changing predictions to
maximum of INT aminoacids. For example, instead of writing the whole modified
protein sequence with potentially hundreds of aminoacids, with -B 1
only an abbreviated version such as 25E..329>25G..94 will be
written.
exclude sites for which EXPRESSION is
true. For valid expressions see EXPRESSIONS.
reference sequence in fasta format
(required)
run even if some sanity checks fail. Currently
the option allows to skip transcripts in malformatted GFFs with incorrect
phase
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
include only sites for which EXPRESSION
is true. For valid expressions see EXPRESSIONS.
switch off haplotype-aware calling, run
localized predictions considering only one VCF record at a time
maximum number of per-haplotype consequences
to consider for each 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 15 which corresponds to one 32-bit integer per diploid
sample, after accounting for values reserved by the BCF specification. Note
that increasing the value leads to increased size of the output BCF.
see Common Options
see Common Options
see Common Options. In addition, a
custom tab-delimited plain text output can be printed ( t).
how to handle unphased heterozygous genotypes:
a
m
r
R
s
take GTs as is, create haplotypes regardless
of phase (0/1 → 0|1)
merge all GTs into a single haplotype (0/1
→ 1, 1/2 → 1)
require phased GTs, throw an error on unphased
heterozygous GTs
create non-reference haplotypes if possible
(0/1 → 1|1, 1/2 → 1|2)
skip unphased heterozygous GTs
suppress warning messages
see Common Options
see Common Options
see Common Options
samples to include or "-" to apply
all variants and ignore samples
see Common Options
see Common Options
see Common Options
see Common Options
# 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 consequences present in either haplotype
bcftools query -f'[%CHROM\t%POS\t%SAMPLE\t%TBCSQ\n]' out.bcf
# 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
3_prime_utr 5_prime_utr coding_sequence feature_elongation frameshift inframe_altering inframe_deletion inframe_insertion intergenic intron missense non_coding splice_acceptor splice_donor splice_region start_lost start_retained stop_gained stop_lost stop_retained synonymous
bcftools filter [OPTIONS] FILE
Apply fixed-threshold filters.exclude sites for which EXPRESSION is
true. For valid expressions see EXPRESSIONS.
filter SNPs within INT base pairs of an
indel or other other variant type. 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..
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..
include only sites for which EXPRESSION
is true. For valid expressions see EXPRESSIONS.
Soft filter regions, prepepend "^"
to negate. Requires -s, --soft-filter.
Soft filter regions listed in a file,
"^" to negate. Requires -s, --soft-filter.
Same as --regions-overlap but for
--mask/--mask-file. See Common Options. [1]
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.
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
annotate FILTER column with STRING or,
with +, a unique filter name generated by the program
("Filter%d").
set genotypes of failed samples to missing
value ( .) or reference allele (0)
see Common Options
see Common Options
see Common Options
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 samples 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.Find sites that can distinguish between at
least NUM sample pairs. If the number is smaller or equal to 1, it is
interpreted as the fraction of pairs. The optional MEM string sets the maximum
memory used for in-memory sorting and DIR is the temporary directory for
external sorting. This option requires also --pairs to be given.
Stop after first record to estimate required
time.
Interpret genotypes and genotype likelihoods
probabilistically. The value of INT represents genotype quality when GT
tag is used (e.g. Q=30 represents one error in 1,000 genotypes and Q=40 one
error in 10,000 genotypes) and is ignored when PL tag is used (in that case an
arbitrary non-zero integer can be provided). See also the -u, --use
option below. If set to 0, the discordance equals to the number of mismatching
genotypes when GT vs GT is compared. Note that the values with and without
-e are not comparable, only values generated with -e 0
correspond to mismatching genotypes. If performance is an issue, set to 0 for
faster run but less accurate results.
VCF/BCF file with reference genotypes to
compare against
Homozygous genotypes only, useful with low
coverage data (requires -g, --genotypes)
Print only top INT matches for each sample, 0
for unlimited. Use negative value to sort by HWE probability rather than the
number of discordant sites. Note that average score is used to determine the
top matches, not absolute values.
Disable calculation of HWE probability to
reduce memory requirements with comparisons between very large number of
sample pairs.
A comma-separated list of sample pairs to
compare. When the -g option is given, the first sample must be from the
query file, the second from the -g file, third from the query file etc
(qry,gt[,qry,gt..]). Without the -g option, the pairs are created the
same way but both samples are from the query file (qry,qry[,qry,qry..])
A file with tab-delimited sample pairs to
compare. The first sample in the pair must come from the query file, the
second from the genotypes file when -g is given
Restrict to comma-separated list of regions,
see Common Options
Restrict to regions listed in a file, see
Common Options
see Common Options
see Common Options
see Common Options
see Common Options
specifies which tag to use in the query file
(TAG1) and the -g (TAG2) file. By default, the PL tag is
used in the query file and GT in the -g file when available.
# Check discordance of all samples from B against all sample in A bcftools gtcheck -g A.bcf B.bcf # Limit comparisons to the fiven list of samples bcftools gtcheck -s gt:a1,a2,a3 -s qry:b1,b2 -g A.bcf B.bcf # Compare only two pairs a1,b1 and a1,b2 bcftools gtcheck -p a1,b1,a1,b2 -g A.bcf B.bcf
bcftools head [ OPTIONS] [FILE]
By default, prints all headers from the specified input file to standard output in VCF format. The input file may be in VCF or BCF format; if no FILE is specified, standard input will be read. With appropriate options, only some of the headers and/or additionally some of the variant records will be printed.Options:
-h, --header INTDisplay only the first INT header
lines. By default, all header lines are displayed.
Also display the first INT variant
records. By default, no variant records are displayed.
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, --csigenerate CSI-format index for VCF/BCF files
[default]
overwrite index if it already exists
set minimal interval size for CSI indices to
2^INT; default: 14
output file name. If not set, then the index
will be created using the input file name plus a .csi or .tbi
extension
generate TBI-format index for VCF files
see Common Options
Stats options:
-a, --allUsed in conjunction with -s, --stats,
print per contig stats for all contigs, even those with zero records and those
for which no stats are recorded in the index file (shown as .).
print the number of records based on the CSI
or TBI index files
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 by default.
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.see Common Options
output positions present only in the first
file but missing in the others
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.
see Common Options
include only sites for which EXPRESSION
is true. See discussion of -e, --exclude above.
output positions present in this many (=),
this many or more (+), this many or fewer (-), or the exact same (~)
files
see Common Options. When several files
are being output, their names are controlled via -p instead.
see Common Options
if given, subset each of the input files
accordingly. See also -w.
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
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
bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e- A.vcf.gz B.vcf.gz C.vcf.gz -n +2 -p dir
bcftools isec -p dir -n=2 -w1 A.vcf.gz B.vcf.gz
bcftools isec -p dir -n-1 -c all A.vcf.gz B.vcf.gz
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 five samples named S1, S2, S3, 2:S3 and S4.if the merged files contain duplicate samples
names, proceed anyway. Duplicate sample names will be resolved by prepending
the index of the file as it appeared on the command line to the conflicting
sample name (see 2:S3 in the above example).
print only merged header and exit
use the VCF header in the provided text
FILE
assume genotypes at missing sites are
0/0
see Common Options
Set the output record to PASS if any of the
inputs is PASS ( x), or apply all filters ( +), which is the
default.
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.
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.
Read file names from FILE, one file
name per line.
Sites with many alternate alleles can require
extremely large storage space which can exceed the 2GB size limit
representable by BCF. This is caused by Number=G tags (such as FORMAT/PL)
which store a value for each combination of reference and alternate alleles.
The -L, --local-alleles option allows to replace such tags with a
localized tag (FORMAT/LPL) which only includes a subset of alternate alleles
relevant for that sample. A new FORMAT/LAA tag is added which lists 1-based
indices of the alternate alleles relevant (local) for the current sample. The
number INT gives the maximum number of alternate alleles that can be
included in the PL tag. The default value is 0 which disables the feature and
outputs values for all alternate alleles.
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 snp-ins-del .. allow multiallelic SNVs, insertions, deletions, but don't mix them -m id .. merge by ID
the option allows to merge files without
indexing them first. In order for this option to work, the user must ensure
that the input files have chromosomes in the same order and consistent with
the order of sequences in the VCF header.
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
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.Input options
-6, --illumina1.3+Assume the quality is in the Illumina 1.3+
encoding.
Do not skip anomalous read pairs in variant
calling.
List of input alignment files, one file per
line [null]
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.
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 position, the new mapping
quality is about sqrt((INT-q)/INT)*INT. A zero value (the default) disables
this functionality.
Run the BAQ algorithm on all reads, not just
those in problematic regions. This matches the behaviour for Bcftools 1.12 and
earlier.
By default mpileup uses heuristics to decide when to apply the BAQ algorithm.
Most sequences will not be BAQ adjusted, giving a CPU time closer to --no-BAQ,
but it will still be applied in regions with suspected problematic alignments.
This has been tested to work well on single sample data with even allele
frequency, but the reliability is unknown for multi-sample calling and for low
allele frequency variants so full BAQ is still recommended in those
scenarios.
At a position, read maximally INT reads
per input file. Note that the original samtools mpileup command had a
minimum value of 8000/n where n was the number of input files
given to mpileup. This means that in samtools mpileup the default was
highly likely to be increased and the -d parameter would have an effect
only once above the cross-sample minimum of 8000. This behavior was
problematic when working with a combination of single- and multi-sample bams,
therefore in bcftools mpileup the user is given the full control (and
responsibility), and an informative message is printed instead [250]
Recalculate BAQ on the fly, ignore existing BQ
tags
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]
Do not require the --fasta-ref
option.
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
Minimum mapping quality for an alignment to be
used [0]
Minimum base quality for a base to be
considered [13]
Caps the base quality to a maximum value [60].
This can be particularly useful on technologies that produce overly optimistic
high qualities, leading to too many false positives or incorrect genotype
assignments.
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
As for -r, --regions, but regions read
from FILE; see Common Options
see Common Options
Ignore RG tags. Treat all reads in one
alignment file as one sample.
Skip reads with all of the FLAG bits set
[null]
Skip reads with any of the FLAG bits set. This
option replaces and is synonymous to the deprecated --ff, --excl-flags
[UNMAP,SECONDARY,QCFAIL,DUP]
Skip reads with all of the FLAG bits unset.
This option replaces and is synonymous to the deprecated --rf,
--incl-flags [null]
Skip reads with any of the FLAG bits unset
[null]
list of sample names. See Common
Options
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".
see Common Options
see Common Options
see Common Options
Disable read-pair overlap detection.
Set the random number seed used when
sub-sampling deep regions [0].
Output options
-a, --annotate LISTComma-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)
FORMAT/SCR .. Number of soft-clipped reads (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)
INFO/SCR .. Number of soft-clipped reads (Number=1,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)
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.
see Common Options
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.)
see Common Options
see Common Options
The the previous Mann-Whitney U test score
from version 1.12 and earlier. This is a probability score, but importantly it
folds probabilities above or below the desired score into the same P. The new
Mann-Whitney U test score is a "Z score", expressing the score as
the number of standard deviations away from the mean (with zero being matching
the mean). It keeps both positive and negative values. This can be important
for some tests where errors are asymmetric.
This option changes the INFO field names produced back to the ones used by the earlier Bcftools releases. For excample BQBZ becomes BQB.
Options for SNP/INDEL genotype likelihood computation
-X, --config STRSpecify a platform specific configuration
profile. The profile should be one of 1.12, illumina, ont
or pacbio-ccs. Settings applied are as follows:
1.12 -Q13 -h100 -m1 illumina [ default values ] ont -B -Q5 --max-BQ 30 -I pacbio-ccs -D -Q5 --max-BQ 50 -F0.1 -o25 -e1 -M99999
What to do with ambiguous indel reads that do
not span an entire short tandem repeat region: discard ambiguous reads from
calling and do not increment high-quality AD depth counters ( drop),
exclude from calling but increment AD counters proportionally ( incAD),
exclude from calling and increment the first value of the AD counter (
incAD0) [ drop]
Phred-scaled gap extension sequencing error
probability. Reducing INT leads to longer indels [20]
Minimum fraction of gapped reads [0.002]
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 [500] Increasing this informs the caller
that indels in long homopolymers are more likely genuine and less likely to be
sequencing artifacts. Hence increasing tandem-qual will have higher recall and
lower precision. Bcftools 1.12 and earlier had a default of 100, which was
tuned around more error prone instruments. Note changing this may have a minor
impact on SNP calling too. For maximum SNP calling accuracy, it may be
preferable to adjust this lower again, although this will adversely affect
indels.
Skews the indel scores up or down, trading
recall (low false-negative) vs precision (low false-positive) [1.0]. In
Bcftools 1.12 and earlier this parameter didn’t exist, but had an
implied value of 1.0. If you are planning to do heavy filtering of variants,
selecting the best quality ones only (favouring precision over recall), it is
advisable to set this lower (such as 0.75) while higher depth samples or where
you favour recall rates over precision may work better with a higher value
such as 2.0.
Indel window size to use when assessing the
quality of candidate indels. Note that although the window size approximately
corresponds to the maximum indel size considered, it is not an exact threshold
[110]
Do not perform INDEL calling
Skip INDEL calling if the average per-sample
depth is above INT [250]
Minimum number gapped reads for indel
candidates INT [1]
The maximum read length permitted by the BAQ
algorithm [500]. Variants are still called on longer reads, but they will not
be passed through the BAQ method. This limit exists to prevent excessively
long BAQ times and high memory usage. Note if partial BAQ is enabled with
-D then raising this parameter will likely not have a significant a CPU
cost.
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]
Apply -m and -F thresholds per
sample to increase sensitivity of calling. By default both options are applied
to reads pooled from all samples.
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.Decompose complex variants, e.g. split MNVs
into consecutive SNVs. See also --atom-overlaps and
--old-rec-tag.
Alleles missing because of an overlapping
variant can be set either to missing (.) or to the star alele (*), as
recommended by the VCF specification. IMPORTANT: Note that asterisk is
expaneded by shell and must be put in quotes or escaped by a backslash:
# Before atomization:
100 CC C,GG 1/2
# After:
# bcftools norm -a .
100 C G ./1
100 CC C 1/.
101 C G ./1
# After:
# bcftools norm -a '*'
# bcftools norm -a \*
100 C G,* 2/1
100 CC C,* 1/2
101 C G,* 2/1
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.
Also note, and this cannot be stressed enough, that s will NOT fix
strand issues in your VCF, do NOT use it for that purpose!!! (Instead see
<http://samtools.github.io/bcftools/howtos/plugin.af-dist.html>
and
<http://samtools.github.io/bcftools/howtos/plugin.fixref.html>.)
If a record is present multiple times, output
only the first instance. See also --collapse in Common
Options.
If a record is present in multiple files,
output only the first instance. Alias for -d none, deprecated.
reference sequence. Supplying this option will
turn on left-alignment and normalization, however, see also the
--do-not-normalize option below.
try to proceed with -m- even if
malformed tags with incorrect number of fields are encountered, discarding
such tags. (Experimental, use at your own risk.)
keep vector sum constant when splitting
multiallelic sites. Only AD tag is currently supported. See also
<https://github.com/samtools/bcftools/issues/360>
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.
see Common Options
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
Add INFO/STR annotation with the original
record. The format of the annotation is CHROM|POS|REF|ALT|USED_ALT_IDX.
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
when merging (-m+), merged site is PASS
only if all sites being merged PASS
see Common Options
see Common Options
see Common Options
see Common Options
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 EXPRESSIONexclude sites for which EXPRESSION is
true. For valid expressions see EXPRESSIONS.
include only sites for which EXPRESSION
is true. For valid expressions see EXPRESSIONS.
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
VCF output options:
--no-versionsee Common Options
see Common Options
see Common Options
see Common Options
Plugin options:
-h, --helplist plugin’s options
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.
print debugging information to debug plugin
failure
print version string and exit
List of plugins coming with the distribution:
ad-biasfind positions with wildly varying ALT allele
frequency (Fisher test on FMT/AD)
add VariantKey INFO fields VKX and RSX
collect AF deviation stats and GT probability
distribution given AF and assuming HWE
count the frequency of the length of REF, ALT
and REF+ALT
check if ploidy of samples is consistent for
all sites
print samples without genotypes in a region or
chromosome
color shared chromosomal segments, requires
trio VCF with phased GTs
runs a basic association test, per-site or in
a region, and checks for novel alleles and genotypes in two groups of samples.
Adds the following INFO annotations:
•PASSOC .. Fisher’s exact test
probability of genotypic association (REF vs non-REF allele)
•FASSOC .. proportion of non-REF allele
in controls and cases
•NASSOC .. number of control-ref,
control-alt, case-ref and case-alt alleles
•NOVELAL .. lists samples with a novel
allele not observed in the control group
•NOVELGT .. lists samples with a novel
genotype not observed in the control group
a minimal plugin which counts number of SNPs,
Indels, and total number of sites.
print genotype dosage. By default the plugin
searches for PL, GL and GT, in that order.
fill INFO or REF field based on values in a
fasta file
set various INFO tags. The list of tags
supported in this version:
•INFO/AC Number:A Type:Integer ..
Allele count in genotypes
•INFO/AC_Hom Number:A Type:Integer ..
Allele counts in homozygous genotypes
•INFO/AC_Het Number:A Type:Integer ..
Allele counts in heterozygous genotypes
•INFO/AC_Hemi Number:A Type:Integer ..
Allele counts in hemizygous genotypes
•INFO/AF Number:A Type:Float .. Allele
frequency
•INFO/AN Number:1 Type:Integer .. Total
number of alleles in called genotypes
•INFO/ExcHet Number:A Type:Float ..
Test excess heterozygosity; 1=good, 0=bad
•INFO/END Number:1 Type:Integer .. End
position of the variant
•INFO/F_MISSING Number:1 Type:Float ..
Fraction of missing genotypes
•INFO/HWE Number:A Type:Float .. HWE
test (PMID:15789306); 1=good, 0=bad
•INFO/MAF Number:A Type:Float .. Minor
Allele frequency
•INFO/NS Number:1 Type:Integer ..
Number of samples with data
•INFO/TYPE Number:. Type:String .. The
record type (REF,SNP,MNP,INDEL,etc)
•FORMAT/VAF Number:A Type:Float .. The
fraction of reads with the alternate allele, requires FORMAT/AD or
ADF+ADR
•FORMAT/VAF1 Number:1 Type:Float .. The
same as FORMAT/VAF but for all alternate alleles cumulatively
•TAG=func(TAG) Number:1 Type:Integer ..
Experimental support for user-defined expressions such as
"DP=sum(DP)"
sets correct ploidy
determine and fix strand orientation
annotate frameshift indels
count genotype intersections across all
possible sample subsets in a vcf file
output only sites where the requested samples
all exclusively share a genotype
determine sample sex by checking genotype
likelihoods (GL,PL) or genotypes (GT) in the non-PAR region of chrX.
compress gVCF file by resizing non-variant
blocks according to specified criteria
add imputation information metrics to the INFO
field based on selected FORMAT tags
calculates per-sample or de novo indels stats.
The usage and format is similar to smpl-stats and
trio-stats
compare two files and set non-identical
genotypes to missing
count Mendelian consistent / inconsistent
genotypes.
sets missing genotypes ("./.") to
ref allele ("0/0" or "0|0")
determine parental origin of a CNV
region
prune sites by missingness, allele frequency
or linkage disequilibrium. Alternatively, annotate sites with r2,
Lewontin’s D' (PMID:19433632), Ragsdale’s D
(PMID:31697386).
remove overlapping variants and duplicate
sites
intended as an inverse to bcftools concat,
scatter VCF by chunks or regions, creating multiple VCFs.
general tool to set genotypes according to
rules requested by the user
calculates basic per-sample stats. The usage
and format is similar to indel-stats and trio-stats.
split VCF by sample, creating single- or
multi-sample VCFs
extract fields from structured annotations
such as INFO/CSQ created by bcftools/csq or VEP. These can be added as a new
INFO field to the VCF or in a custom text format. See
<http://samtools.github.io/bcftools/howtos/plugin.split-vep.html> for
more.
Convert between similar tags, such as GL,PL,GP
or QR,QA,QS.
screen variants for possible de-novo mutations
in trios
calculate transmission rate in trio children.
The usage and format is similar to indel-stats and
smpl-stats.
calculate phase switch rate in trio samples,
children samples must have phased GTs
annotate sites with the distance to the
nearest variant
generate unsorted VariantKey-RSid index files
in hexadecimal format
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 # Run a plugin from an explicit location bcftools +/path/to/counts.so 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 pathoutput directory
see Common Options
see Common Options
see Common Options
sample name
see Common Options
see Common Options
see Common Options
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 floatthe minimum peak size considered as a good
match can be from the interval [0,1] where larger is stricter
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.
threshold for goodness of fit (normalized
absolute deviation), smaller is stricter
include also the AA peak in CN2 and CN3
evaluation. This usually requires increasing -f.
minimum distinguishable fraction of aberrant
cells. The experience shows that trustworthy are estimates of 20% and
more.
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.exclude sites for which EXPRESSION is
true. For valid expressions see EXPRESSIONS.
continue even when some samples requested via
-s/-S do not exist
learn by example, see below
print header
include only sites for which EXPRESSION
is true. For valid expressions see EXPRESSIONS.
list sample names and exit
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
do not throw an error if there are undefined
tags in the format string, print "." instead
process multiple VCFs listed in the file
Format:
%CHROM The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER)
%END End position of the REF allele
%END0 End position of the REF allele in 0-based coordinates
%FIRST_ALT Alias for %ALT{0}
%FORMAT Prints all FORMAT fields or a subset of samples with -s or -S
%GT Genotype (e.g. 0/1)
%INFO Prints the whole INFO column
%INFO/TAG Any tag in the INFO column
%IUPACGT Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
%LINE Prints the whole line
%MASK Indicates presence of the site in other files (with multiple files)
%N_PASS(expr) Number of samples that pass the filtering expression (see *<<expressions,EXPRESSIONS>>*)
%POS0 POS in 0-based coordinates
%PBINOM(TAG) Calculate phred-scaled binomial probability, the allele index is determined from GT
%SAMPLE Sample name
%TAG{INT} Curly brackets to print a subfield (e.g. INFO/TAG{1}, the indexes are 0-based)
%TBCSQ Translated FORMAT/BCSQ. See the csq command above for explanation and examples.
%TGT Translated genotype (e.g. C/A)
%TYPE Variant type (REF, SNP, MNP, INDEL, BND, OTHER)
[] Format fields must be enclosed in brackets to loop over all samples
\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]'
# Print phred-scaled binomial probability from FORMAT/AD tag for all heterozygous genotypes bcftools query -i'GT="het"' -f'[%CHROM:%POS %SAMPLE %GT %PBINOM(AD)\n]' file.vcf
# Print the second value of AC field if bigger than 10. Note the (unfortunate) difference in
# index subscript notation: formatting expressions (-f) uses "{}" while filtering expressions
# (-i) use "[]". This is for historic reasons and backward-compatibility.
bcftools query -f '%AC{1}\n' -i 'AC[1]>10' file.vcf.gz
bcftools reheader [ OPTIONS] file.vcf.gz
Modify header of VCF/BCF files, change sample names.add to the header contig names and their
lengths from the provided fasta index file (.fai). Lengths of existing contig
lines will be updated and contig lines not present in the fai file will be
removed
new VCF header
see Common Options
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".
template for temporary file names, used with
-f
see Common Options
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 FLOATin case allele frequency is not known, use the
FLOAT. By default, sites where allele frequency cannot be determined,
or is 0, are skipped.
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.
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
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.
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 sites for which EXPRESSION is
true. For valid expressions see EXPRESSIONS.
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 only sites for which EXPRESSION
is true. For valid expressions see EXPRESSIONS.
skip indels as their genotypes are usually
enriched for errors
genetic map in the format required also by
IMPUTE2. Only the first and third column are used (position and
Genetic_Map(cM)). The FILE can be a single file or a file mask, where
string "{CHROM}" is replaced with chromosome name.
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).
Write output to the FILE, by default
the output is printed on stdout
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.
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
HMM Options:
-a, --hw-to-az FLOATP(AZ|HW) transition probability from AZ
(autozygous) to HW (Hardy-Weinberg) state
P(HW|AZ) transition probability from HW to AZ
state
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.
see Common Options
see Common Options
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.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)
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.
consider only the 1st alternate allele at
multiallelic sites
see Common Options
ranges of depth distribution: min, max, and
size of the bin
produce verbose per-site and per-sample
output
exclude sites for which EXPRESSION is
true. For valid expressions see EXPRESSIONS.
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
see Common Options
faidx indexed reference sequence file to
determine INDEL context
include only sites for which EXPRESSION
is true. For valid expressions see EXPRESSIONS.
collect stats separately for sites which have
the ID column set ("known sites") or which do not have the ID column
set ("novel sites").
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
collect Ts/Tv stats for any tag using the
given binning [0:1:100]
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-genotypesdrop individual genotype information (after
subsetting if -s option is set)
output the VCF header only (see also
bcftools head)
suppress the header in VCF output
output both VCF header and records (this is
the default, but the option is useful for explicitness or to reset the effects
of -h or -H)
compression level. 0 stands for uncompressed,
1 for best speed and 9 for best compression.
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
see Common Options
Subset options:
-a, --trim-alt-allelesremove alleles not seen in the genotype fields
from the ALT column. Note that if no alternate allele remains after trimming,
the record itself is not removed but ALT is set to ".". If the
option -s or -S is given, removes alleles not seen in the
subset. INFO and FORMAT tags declared as Type=A, G or R will be trimmed as
well.
only warn about unknown subset samples
do not (re)calculate INFO fields for the
subset (currently INFO/AC and INFO/AN)
see Common Options. Note that it is
possible to create multiple subsets simultaneously using the split
plugin.
see Common Options. Note that it is
possible to create multiple subsets simultaneously using the split
plugin.
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 calculated from INFO/AC and INFO/AN when available or FORMAT/GT otherwise. However, it will not attempt to use any other existing field, like INFO/AF for example. For that, use --exclude AF<0.1 instead.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.
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.
exclude sites for which EXPRESSION is
true. For valid expressions see EXPRESSIONS.
see Common Options
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.
include sites for which EXPRESSION is
true. For valid expressions see EXPRESSIONS.
print known sites only (ID column is not
".")
print sites with at least INT alleles
listed in REF and ALT columns
print sites with at most INT alleles
listed in REF and ALT columns. Use -m2 -M2 -v snps to only view
biallelic SNPs.
print novel sites only (ID column is
".")
print sites where all samples are phased.
Haploid genotypes are considered phased. Missing genotypes considered unphased
unless the phased bit is set.
exclude sites where all samples are
phased
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.
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.
print sites without a called genotype
exclude sites without a called genotype
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.
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.
print sites where only the subset samples
carry an non-reference allele. Requires --samples or
--samples-file.
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.•numerical constants, string constants,
file names (this is currently supported only to filter by the ID column)
1, 1.0, 1e-4 "String" @file_name
•arithmetic operators (addition,
multiplication, subtraction, division, modulo)
+, *, -, /, %
•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. See also the
examples below and the filtering tutorial
<http://samtools.github.io/bcftools/howtos/filtering.html> about the
distinction between "&&" vs "&" and
"||" vs "|".
&&, &, ||, |
•INFO tags, FORMAT tags, column names
INFO/DP or DP FORMAT/DV, FMT/DV, or DV FILTER, QUAL, ID, CHROM, POS, REF, ALT[0]
•the FILTER column can be queried as
follows:
FILTER="PASS" FILTER="." FILTER="A" .. exact match, for example "A;B" does not pass FILTER="A;B" .. exact match, "A;B" and "B;A" pass, everything else fails FILTER!="A" .. exact match, for example "A;B" does pass FILTER~"A" .. subset match, for example both "A" and "A;B" pass FILTER~"A;B" .. subset match, pass only if both "A" and "B" are present FILTER!~"A" .. complement match, for example both "A" and "A;B" fail FILTER!~"A;B" .. complement match, fail if both "A" and "B" are present
•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 (".|.", "./.",
".", "0|.") using these expressions
GT="mis", 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,overlap). 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"
•with many samples it can be more
practical to provide a file with sample names, one sample name per line
GT[@samples.txt]="het" & binom(AD)<0.01
•function on FORMAT tags (over samples)
and INFO tags (over vector fields): maximum; minimum; arithmetic mean (AVG is
synonymous with MEAN); median; standard deviation from mean; sum; string
length; absolute value; number of elements:
Note that functions above evaluate to a single value across all samples and are
intended to select sites, not samples, even when applied on FORMAT tags.
However, when prefixed with SMPL_ (or "s" for brevity, e.g. SMPL_MAX
or sMAX), they will evaluate to a vector of per-sample values when applied on
FORMAT tags:
MAX, MIN, AVG, MEAN, MEDIAN, STDEV, SUM, STRLEN, ABS, COUNT
SMPL_MAX, SMPL_MIN, SMPL_AVG, SMPL_MEAN, SMPL_MEDIAN, SMPL_STDEV, SMPL_SUM, sMAX, sMIN, sAVG, sMEAN, sMEDIAN, sSTDEV, sSUM
•two-tailed binomial test. Note that
for N=0 the test evaluates to a missing value and when FORMAT/GT is used to
determine the vector indices, it evaluates to 1 for homozygous genotypes.
binom(FMT/AD) .. GT can be used to determine the correct index binom(AD[0],AD[1]) .. or the fields can be given explicitly phred(binom()) .. the same as binom but phred-scaled
•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; indel length
(deletions negative, insertions positive)
N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN, N_MISSING, F_MISSING, ILEN
•the number (N_PASS) or fraction
(F_PASS) of samples which pass the expression
N_PASS(GQ>90 & GT!="mis") > 90 F_PASS(GQ>90 & GT!="mis") > 0.9
•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
•String comparisons and regular
expressions are case-insensitive
•Comma in strings is interpreted as a
separator and when multiple values are compared, the OR logic is used.
Consequently, the following two expressions are equivalent but not the third:
-i 'TAG="hello,world"' -i 'TAG="hello" || TAG="world"' -i 'TAG="hello" && TAG="world"'
•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
MIN(DV)>5 .. selects the whole site, evaluates min across all values and samples
SMPL_MIN(DV)>5 .. selects matching samples, evaluates within samples
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 .. no homozygous genotypes at the site
AVG(GQ)>50 .. average (arithmetic mean) of genotype qualities bigger than 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.
bcftools view -i '%ID!="." & MAF[0]<0.01'
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.Merge vcfstats files to STDOUT, skip
plotting.
The output directory. This directory will be
created if it does not exist.
Skip the PDF creation step.
Rasterize PDF images for faster rendering.
This is the default and the opposite of -v, --vectors.
Use sample names for xticks rather than
numeric IDs.
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.
Generate vector graphics for PDF images, the
opposite of -r, --rasterize.
Main title for the PDF.
# Generate the stats bcftools stats -s - > file.vchk
# Plot the stats plot-vcfstats -p outdir file.vchk
# The final looks can be customized by editing the generated # 'outdir/plot.py' script and re-running manually cd outdir && python plot.py && pdflatex summary.tex
PERFORMANCE
HTSlib was designed with BCF format in mind. When parsing VCF files, all records are internally converted into BCF representation. Simple operations, like removing a single column from a VCF file, can be therefore done much faster with standard UNIX commands, such as awk or cut. Therefore it is recommended to use BCF as input/output format whenever possible to avoid large overhead of the VCF → BCF → VCF conversion.BUGS
Please report any bugs you encounter on the github website: <http://github.com/samtools/bcftools>AUTHORS
Heng Li from the Sanger Institute wrote the original C version of htslib, samtools and bcftools. Bob Handsaker from the Broad Institute implemented the BGZF library. Petr Danecek, Shane McCarthy and John Marshall are maintaining and further developing bcftools. Many other people contributed to the program and to the file format specifications, both directly and indirectly by providing patches, testing and reporting bugs. We thank them all.RESOURCES
BCFtools GitHub website: <http://github.com/samtools/bcftools>COPYING
The MIT/Expat License or GPL License, see the LICENSE document for details. Copyright (c) Genome Research Ltd.| 2022-08-18 |