COMMANDS AND OPTIONS
Common Options
The following options are common to many bcftools commands. See usage for
specific commands to see if they apply.
-
FILE
-
Files can be both VCF or BCF, uncompressed or BGZF-compressed. The file "-"
is interpreted as standard input. Some tools may require tabix- or
CSI-indexed files.
-
-c, --collapse snps|indels|both|all|some|none|id
Controls how to treat records with duplicate positions and defines compatible
records across multiple input files. Here by "compatible" we mean records which
should be considered as identical by the tools. For example, when performing
line intersections, the desire may be to consider as identical all sites with
matching positions (bcftools isec -c all), or only sites with matching variant
type (bcftools isec -c snps -c indels), or only sites with all alleles
identical (bcftools isec -c none).
-
none
-
only records with identical REF and ALT alleles are compatible
-
some
-
only records where some subset of ALT alleles match are compatible
-
all
-
all records are compatible, regardless of whether the ALT alleles
match or not. In the case of records with the same position, only
the first will be considered and appear on output.
-
snps
-
any SNP records are compatible, regardless of whether the ALT
alleles match or not. For duplicate positions, only the first SNP
record will be considered and appear on output.
-
indels
-
all indel records are compatible, regardless of whether the REF
and ALT alleles match or not. For duplicate positions, only the
first indel record will be considered and appear on output.
-
both
-
abbreviation of "-c indels -c snps"
-
id
-
only records with identical ID column are compatible.
Supported by bcftools merge only.
-
-f, --apply-filters LIST
-
Skip sites where FILTER column does not contain any of the strings listed
in LIST. For example, to include only sites which have no filters set,
use -f .,PASS.
-
--no-version
-
Do not append version and command line information to the output VCF header.
-
-o, --output FILE
-
When output consists of a single stream, write it to FILE rather than
to standard output, where it is written by default.
-
-O, --output-type b|u|z|v
-
Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF (v).
Use the -Ou option when piping between bcftools subcommands to speed up
performance by removing unnecessary compression/decompression and
VCF←→BCF conversion.
-
-r, --regions chr|chr:pos|chr:beg-end|chr:beg-[,…]
-
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.
-
-R, --regions-file FILE
-
Regions can be specified either on command line or in a VCF, BED, or
tab-delimited file (the default). The columns of the tab-delimited file
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.
-
-s, --samples [^]LIST
-
Comma-separated list of samples to include or exclude if prefixed
with "^".
The sample order is updated to reflect that given on the command line.
Note that in general tags such as INFO/AC, INFO/AN, etc are not updated
to correspond to the subset samples. bcftools view is the
exception where some tags will be updated (unless the -I, --no-update
option is used; see bcftools view documentation). To use updated
tags for the subset in another command one can pipe from view into
that command. For example:
bcftools view -Ou -s sample1,sample2 file.vcf | bcftools query -f %INFO/AC\t%INFO/AN\n
-
-S, --samples-file FILE
-
File of sample names to include or exclude if prefixed with "^".
One sample per line. See also the note above for the -s, --samples
option.
The sample order is updated to reflect that given in the input file.
The command bcftools call accepts an optional second
column indicating ploidy (0, 1 or 2) or sex (as defined by
--ploidy, for example "F" or "M"), for example:
sample1 1
sample2 2
sample3 2
or
sample1 M
sample2 F
sample3 F
If the second column is not present, the sex "F" is assumed.
With bcftools call -C trio, PED file is expected.
The program ignores the first column and the last indicates sex (1=male, 2=female), for example:
ignored_column daughterA fatherA motherA 2
ignored_column sonB fatherB motherB 1
-
-t, --targets [^]chr|chr:pos|chr:from-to|chr:from-[,…]
-
Similar as -r, --regions, but the next position is accessed by streaming the
whole VCF/BCF rather than using the tbi/csi index. Both -r and -t options
can be applied simultaneously: -r uses the index to jump to a region
and -t discards positions which are not in the targets. Unlike -r, targets
can be prefixed with "^" to request logical complement. For example, "^X,Y,MT"
indicates that sequences X, Y and MT should be skipped.
Yet another difference between the -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. Note that -t cannot be used in combination with -T.
-
-T, --targets-file [^]FILE
-
Same -t, --targets, but reads regions from a file. Note that -T
cannot be used in combination with -t.
-
-
With the call -C alleles command, third column of the targets file must
be comma-separated list of alleles, starting with the reference allele.
Note that the file must be compressed and index.
Such a file can be easily created from a VCF using:
bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
-
--threads INT
-
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.
-
-a, --annotations file
-
Bgzip-compressed and tabix-indexed file with annotations. The file
can be VCF, BED, or a tab-delimited file with mandatory columns CHROM, POS
(or, alternatively, FROM and TO), optional columns REF and ALT, and arbitrary
number of annotation columns. BED files are expected to have
the ".bed" or ".bed.gz" suffix (case-insensitive), otherwise a tab-delimited file is assumed.
Note that in case of tab-delimited file, the coordinates POS, FROM and TO are
one-based and inclusive. When REF and ALT are present, only matching VCF
records will be annotated.
When multiple ALT alleles are present in the annotation file (given as
comma-separated list of alleles), at least one must match one of the
alleles in the corresponding VCF record. Similarly, at least one
alternate allele from a multi-allelic VCF record must be present in the
annotation file.
Missing values can be added by providing "." in place of actual value.
Note that flag types, such as "INFO/FLAG", can be annotated by including
a field with the value "1" to set the flag, "0" to remove it, or "." to
keep existing flags.
See also -c, --columns and -h, --header-lines.
# Sample annotation file with columns CHROM, POS, STRING_TAG, NUMERIC_TAG
1 752566 SomeString 5
1 798959 SomeOtherString 6
# etc.
-
--collapse snps|indels|both|all|some|none
-
Controls how to match records from the annotation file to the target VCF.
Effective only when -a is a VCF or BCF.
See Common Options for more.
-
-c, --columns list
-
Comma-separated list of columns or tags to carry over from the annotation file
(see also -a, --annotations). If the annotation file is not a VCF/BCF,
list describes the columns of the annotation file and must include CHROM,
POS (or, alternatively, FROM and TO), and optionally REF and ALT. Unused
columns which should be ignored can be indicated by "-".
If the annotation file is a VCF/BCF, only the edited columns/tags must be present and their
order does not matter. The columns ID, QUAL, FILTER, INFO and FORMAT
can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG",
and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG".
The imported VCF annotations can be renamed as "DST_TAG:=SRC_TAG" or "FMT/DST_TAG:=FMT/SRC_TAG".
To carry over all INFO annotations, use "INFO". To add all INFO annotations except
"TAG", use "^INFO/TAG". By default, existing values are replaced.
To add annotations without overwriting existing values (that is, to add missing tags or
add values to existing tags with missing values), use "+TAG" instead of "TAG".
To append to existing values (rather than replacing or leaving untouched), use "=TAG"
(instead of "TAG" or "+TAG").
To replace only existing values without modifying missing annotations, use "-TAG".
If the annotation file is not a VCF/BCF, all new annotations must be
defined via -h, --header-lines.
See also the -l, --merge-logic option.
-
-C, --columns-file file
-
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.
-
-e, --exclude EXPRESSION
-
exclude sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
--force
-
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.
-
-h, --header-lines file
-
Lines to append to the VCF header, see also -c, --columns and -a, --annotations. For example:
##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">
-
-I, --set-id [+]FORMAT
-
assign ID on the fly. The format is the same as in the query
command (see below). By default all existing IDs are replaced. If the
format string is preceded by "+", only missing IDs will be set. For example,
one can use
bcftools annotate --set-id +'%CHROM\_%POS\_%REF\_%FIRST_ALT' file.vcf
-
-i, --include EXPRESSION
-
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-k, --keep-sites
-
keep sites which do not pass -i and -e expressions instead of discarding them
-
-l, --merge-logic tag:'first'|append|append-missing|unique|sum|avg|min|max[,…]
-
if multiple regions overlap a single record, the 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.
-
-m, --mark-sites TAG
-
annotate sites which are present ("+") or absent ("-") in the -a file with a new INFO/TAG flag
-
--no-version
-
see Common Options
-
-o, --output FILE
-
see Common Options
-
-O, --output-type b|u|z|v
-
see Common Options
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file file
-
see Common Options
-
--rename-annots file
-
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-chrs file
-
rename chromosomes according to the map in file, with
"old_name new_name\n" pairs separated by whitespaces, each on a separate
line.
-
-s, --samples [^]LIST
-
subset of samples to annotate, see also Common Options
-
-S, --samples-file FILE
-
subset of samples to annotate. If the samples are named differently in the
target VCF and the -a, --annotations VCF, the name mapping can be
given as "src_name dst_name\n", separated by whitespaces, each pair on a
separate line.
-
--single-overlaps
-
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).
-
--threads INT
-
see Common Options
-
-x, --remove list
-
List of annotations to remove. Use "FILTER" to remove all filters or
"FILTER/SomeFilter" to remove a specific filter. Similarly, "INFO" can
be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags
except GT. To remove all INFO tags except "FOO" and "BAR", use
"^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER).
"INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".
Examples:
# Remove three fields
bcftools annotate -x ID,INFO/DP,FORMAT/DP file.vcf.gz
# Remove all INFO fields and all FORMAT fields except for GT and PL
bcftools annotate -x INFO,^FORMAT/GT,FORMAT/PL file.vcf
# Add ID, QUAL and INFO/TAG, not replacing TAG if already present
bcftools annotate -a src.bcf -c ID,QUAL,+TAG dst.bcf
# Carry over all INFO and FORMAT annotations except FORMAT/GT
bcftools annotate -a src.bcf -c INFO,^FORMAT/GT dst.bcf
# Annotate from a tab-delimited file with six columns (the fifth is ignored),
# first indexing with tabix. The coordinates are 1-based.
tabix -s1 -b2 -e2 annots.tab.gz
bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,POS,REF,ALT,-,TAG file.vcf
# Annotate from a tab-delimited file with regions (1-based coordinates, inclusive)
tabix -s1 -b2 -e3 annots.tab.gz
bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG 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
# 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, but will be added back on popular
demand. The original calling model can be invoked with the -c option.
File format options:
-
--no-version
-
see Common Options
-
-o, --output FILE
-
see Common Options
-
-O, --output-type b|u|z|v
-
see Common Options
-
--ploidy ASSEMBLY[?]
-
predefined ploidy, use list (or any other unused word) to print a list
of all predefined assemblies. Append a question mark to print the actual
definition. See also --ploidy-file.
-
--ploidy-file FILE
-
ploidy definition given as a space/tab-delimited list of
CHROM, FROM, TO, SEX, PLOIDY. The SEX codes are arbitrary and
correspond to the ones used by --samples-file.
The default ploidy can be given using the starred records (see
below), unlisted regions have ploidy 2. The default ploidy definition is
X 1 60000 M 1
X 2699521 154931043 M 1
Y 1 59373566 M 1
Y 1 59373566 F 0
MT 1 16569 M 1
MT 1 16569 F 1
* * * M 2
* * * F 2
Input/output options:
-
-A, --keep-alts
-
output all alternate alleles present in the alignments even if they do not
appear in any of the genotypes
-
-f, --format-fields list
-
comma-separated list of FORMAT fields to output for each sample. Currently
GQ and GP fields are supported. For convenience, the fields can be given
as lower case letters. Prefixed with "^" indicates a request for tag
removal of auxiliary tags useful only for calling.
-
-F, --prior-freqs AN,AC
-
take advantage of prior knowledge of population allele frequencies. The
workflow looks like this:
# Extract AN,AC values from an existing VCF, such 1000Genomes
bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' 1000Genomes.bcf | bgzip -c > AFs.tab.gz
# If the tags AN,AC are not already present, use the +fill-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 [...]
-
-G, --group-samples FILE|-
-
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).
-
-g, --gvcf INT
-
output also gVCF blocks of homozygous REF calls. The parameter INT is the
minimum per-sample depth required to include a site in the non-variant
block.
-
-i, --insert-missed INT
-
output also sites missed by mpileup but present in -T, --targets-file.
-
-M, --keep-masked-ref
-
output sites where REF allele is N
-
-V, --skip-variants snps|indels
-
skip indel/SNP sites
-
-v, --variants-only
-
output variant sites only
Consensus/variant calling options:
-
-c, --consensus-caller
-
the original samtools/bcftools calling method (conflicts with -m)
-
-C, --constrain alleles|trio
-
alleles
-
call genotypes given alleles. See also -T, --targets-file.
-
trio
-
call genotypes given the father-mother-child constraint. See also
-s, --samples and -n, --novel-rate.
-
-m, --multiallelic-caller
-
alternative model for multiallelic and rare-variant calling designed to
overcome known limitations in -c calling model (conflicts with -c)
-
-n, --novel-rate float[,…]
-
likelihood of novel mutation for constrained -C trio calling. The trio
genotype calling maximizes likelihood of a particular combination of
genotypes for father, mother and the child
P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn).
By providing three values, the mutation rate Pn is set explicitly for SNPs,
deletions and insertions, respectively. If two values are given, the first
is interpreted as the mutation rate of SNPs and the second is used to
calculate the mutation rate of indels according to their length as
Pn=float*exp(-a-b*len), where a=22.8689, b=0.2994 for insertions and
a=21.9313, b=0.2856 for deletions [pubmed:23975140]. If only one value is
given, the same mutation rate Pn is used for SNPs and indels.
-
-p, --pval-threshold float
-
with -c, accept variant if P(ref|D) < float.
-
-P, --prior float
-
expected substitution rate, or 0 to disable the prior. Only with -m.
-
-t, --targets file|chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-X, --chromosome-X
-
haploid output for male samples (requires PED file with -s)
-
-Y, --chromosome-Y
-
haploid output for males and skips females (requires PED file with -s)
bcftools cnv [OPTIONS] FILE
Copy number variation caller, requires a VCF annotated with the Illumina’s
B-allele frequency (BAF) and Log R Ratio intensity (LRR) values. The HMM
considers the following copy number states: CN 2 (normal), 1 (single-copy
loss), 0 (complete loss), 3 (single-copy gain).
General Options:
-
-c, --control-sample string
-
optional control sample name. If given, pairwise calling is performed
and the -P option can be used
-
-f, --AF-file file
-
read allele frequencies from a tab-delimited file with the columns CHR,POS,REF,ALT,AF
-
-o, --output-dir path
-
output directory
-
-p, --plot-threshold float
-
call matplotlib to produce plots for chromosomes with quality at least float,
useful for visual inspection of the calls. With -p 0, plots for all chromosomes will be
generated. If not given, a matplotlib script will be created but not called.
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file file
-
see Common Options
-
-s, --query-sample string
-
query sample name
-
-t, --targets LIST
-
see Common Options
-
-T, --targets-file FILE
-
see Common Options
HMM Options:
-
-a, --aberrant float[,float]
-
fraction of aberrant cells in query and control. The hallmark of
duplications and contaminations is the BAF value of heterozygous markers
which is dependent on the fraction of aberrant cells. Sensitivity to
smaller fractions of cells can be increased by setting -a to a lower value. Note
however, that this comes at the cost of increased false discovery rate.
-
-b, --BAF-weight float
-
relative contribution from BAF
-
-d, --BAF-dev float[,float]
-
expected BAF deviation in query and control, i.e. the noise observed
in the data.
-
-e, --err-prob float
-
uniform error probability
-
-l, --LRR-weight float
-
relative contribution from LRR. With noisy data, this option can have big effect
on the number of calls produced. In truly random noise (such as in simulated data),
the value should be set high (1.0), but in the presence of systematic noise
when LRR are not informative, lower values result in cleaner calls (0.2).
-
-L, --LRR-smooth-win int
-
reduce LRR noise by applying moving average given this window size
-
-O, --optimize float
-
iteratively estimate the fraction of aberrant cells, down to the given fraction.
Lowering this value from the default 1.0 to say, 0.3, can help discover more
events but also increases noise
-
-P, --same-prob float
-
the prior probability of the query and the control sample being the same.
Setting to 0 calls both independently, setting to 1 forces the same copy
number state in both.
-
-x, --xy-prob float
-
the HMM probability of transition to another copy number state. Increasing this
values leads to smaller and more frequent calls.
bcftools concat [OPTIONS] FILE1 FILE2 […]
Concatenate or combine VCF/BCF files. All source files must have the same sample
columns appearing in the same order. Can be used, for example, to
concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel
VCF into one. The input files must be sorted by chr and position. The files
must be given in the correct order to produce sorted VCF on output unless
the -a, --allow-overlaps option is specified. With the --naive option, the files
are concatenated without being recompressed, which is very fast..
-
-a, --allow-overlaps
-
First coordinate of the next file can precede last record of the current file.
-
-c, --compact-PS
-
Do not output PS tag at each site, only at the start of a new phase set block.
-
-d, --rm-dups snps|indels|both|all|none
-
Output duplicate records of specified type present in multiple files only once.
Requires -a, --allow-overlaps.
-
-D, --remove-duplicates
-
Alias for -d none
-
-f, --file-list FILE
-
Read file names from FILE, one file name per line.
-
-l, --ligate
-
Ligate phased VCFs by matching phase at overlapping haplotypes.
Note that the option is intended for VCFs with perfect overlap, sites
in overlapping regions present in one but missing in other are dropped.
-
--no-version
-
see Common Options
-
-n, --naive
-
Concatenate VCF or BCF files without recompression. This is very fast but requires
that all files are of the same type (all VCF or all BCF) and have the same headers.
This is because all tags and chromosome names in the BCF body rely on the 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.
-
--naive-force
-
Same as --naive, but header compatibility is not checked. Dangerous, use with caution.
-
-o, --output FILE
-
see Common Options
-
-O, --output-type b|u|z|v
-
see Common Options
-
-q, --min-PQ INT
-
Break phase set if phasing quality is lower than INT
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options. Requires -a, --allow-overlaps.
-
-R, --regions-file FILE
-
see Common Options. Requires -a, --allow-overlaps.
-
--threads INT
-
see Common Options
bcftools consensus [OPTIONS] FILE
Create consensus sequence by applying VCF variants to a reference fasta file.
By default, the program will apply all ALT variants to the reference fasta to
obtain the consensus sequence. Using the --sample (and, optionally,
--haplotype) option will apply genotype (haplotype) calls from FORMAT/GT.
Note that the program does not act as a primitive variant caller and ignores allelic
depth information, such as INFO/AD or FORMAT/AD. For that, consider using the
setGT plugin.
-
-c, --chain FILE
-
write a chain file for liftover
-
-e, --exclude EXPRESSION
-
exclude sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-f, --fasta-ref FILE
-
reference sequence in fasta format
-
-H, --haplotype 1|2|R|A|I|LR|LA|SR|SA|1pIu|2pIu
choose which allele from the FORMAT/GT field to use (the codes are case-insensitive):
-
1
-
the first allele, regardless of phasing
-
2
-
the second allele, regardless of phasing
-
R
-
the REF allele (in heterozygous genotypes)
-
A
-
the ALT allele (in heterozygous genotypes)
-
I
-
IUPAC code for all genotypes
-
LR, LA
-
the longer allele. If both have the same length, use the REF allele (LR), or the ALT allele (LA)
-
SR, SA
-
the shorter allele. If both have the same length, use the REF allele (SR), or the ALT allele (SA)
-
1pIu, 2pIu
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
-
-i, --include EXPRESSION
-
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-I, --iupac-codes
-
output variants in the form of IUPAC ambiguity codes
-
--mark-del CHAR
-
instead of removing sequence, insert CHAR for deletions
-
--mark-ins uc|lc
-
highlight inserted sequence in uppercase (uc) or lowercase (lc), leaving the rest of the sequence as is
-
--mark-snv uc|lc
-
highlight substitutions in uppercase (uc) or lowercase (lc), leaving the rest of the sequence as is
-
-m, --mask FILE
-
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.
-
--mask-with CHAR|lc|uc
-
replace sequence from --mask with CHAR, skipping overlapping variants, or change to lowercase (lc) or uppercase (uc)
-
-M, --missing CHAR
-
instead of skipping the missing genotypes, output the character CHAR (e.g. "?")
-
-o, --output FILE
-
write output to a file
-
-s, --sample NAME
-
apply variants of the given sample
Examples:
# Apply variants present in sample "NA001", output IUPAC codes for hets
bcftools consensus -i -s NA001 -f in.fa in.vcf.gz > out.fa
# Create consensus for one region. The fasta header lines are then expected
# in the form ">chr:from-to".
samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz -o out.fa
bcftools convert [OPTIONS] FILE
GEN/SAMPLE conversion:
-
-G, --gensample2vcf prefix or gen-file,sample-file
-
convert IMPUTE2 output to VCF. The second column must be of the form
"CHROM:POS_REF_ALT" to detect possible strand swaps; IMPUTE2 leaves the
first one empty ("--") when sites from reference panel are filled in. See
also -g below.
-
-g, --gensample prefix or gen-file,sample-file
-
convert from VCF to gen/sample format used by IMPUTE2 and SHAPEIT.
The columns of .gen file format are ID1,ID2,POS,A,B followed by three
genotype probabilities P(AA), P(AB), P(BB) for each sample. In order to
prevent strand swaps, the program uses IDs of the form "CHROM:POS_REF_ALT".
For example:
.gen
----
1:111485207_G_A 1:111485207_G_A 111485207 G A 0 1 0 0 1 0
1:111494194_C_T 1:111494194_C_T 111494194 C T 0 1 0 0 0 1
.sample
-------
ID_1 ID_2 missing
0 0 0
sample1 sample1 0
sample2 sample2 0
-
--tag STRING
-
tag to take values for .gen file: GT,PL,GL,GP
-
--chrom
-
output chromosome in the first column instead of CHROM:POS_REF_ALT
-
--sex FILE
-
output sex column in the sample file. The FILE format is
MaleSample M
FemaleSample F
-
--vcf-ids
-
output VCF IDs in the second column instead of CHROM:POS_REF_ALT
gVCF conversion:
-
--gvcf2vcf
-
convert gVCF to VCF, expanding REF blocks into sites. 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.
-
-f, --fasta-ref file
-
reference sequence in fasta format. Must be indexed with samtools faidx
HAP/SAMPLE conversion:
-
--hapsample2vcf prefix or hap-file,sample-file
-
convert from hap/sample format to VCF. The columns of .hap file are
similar to .gen file above, but there are only two haplotype columns per
sample. Note that the first column of the .hap file is expected to be in
the form "CHR:POS_REF_ALT(_END)?", with the _END being optional for
defining the INFO/END tag when ALT is a symbolic allele, for example:
.hap
----
1:111485207_G_A rsID1 111485207 G A 0 1 0 0
1:111494194_C_T rsID2 111494194 C T 0 1 0 0
1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0
-
--hapsample prefix or hap-file,sample-file
-
convert from VCF to hap/sample format used by IMPUTE2 and SHAPEIT.
The columns of .hap file begin with ID,RSID,POS,REF,ALT. In order to
prevent strand swaps, the program uses IDs of the form
"CHROM:POS_REF_ALT".
-
--haploid2diploid
-
with -h option converts haploid genotypes to homozygous diploid
genotypes. For example, the program will print 0 0 instead of the
default 0 -. This is useful for programs which do not handle haploid
genotypes correctly.
-
--sex FILE
-
output sex column in the sample file. The FILE format is
MaleSample M
FemaleSample F
-
--vcf-ids
-
output VCF IDs instead of "CHROM:POS_REF_ALT" IDs
HAP/LEGEND/SAMPLE conversion:
-
-H, --haplegendsample2vcf prefix or hap-file,legend-file,sample-file
-
convert from hap/legend/sample format used by IMPUTE2 to VCF, see
also -h, --hapslegendsample below.
-
-h, --haplegendsample prefix or hap-file,legend-file,sample-file
-
convert from VCF to hap/legend/sample format used by IMPUTE2 and SHAPEIT.
The columns of .legend file ID,POS,REF,ALT. In order to prevent strand
swaps, the program uses IDs of the form "CHROM:POS_REF_ALT". The .sample
file is quite basic at the moment with columns for population, group and
sex expected to be edited by the user. For example:
.hap
-----
0 1 0 0 1 0
0 1 0 0 0 1
.legend
-------
id position a0 a1
1:111485207_G_A 111485207 G A
1:111494194_C_T 111494194 C T
.sample
-------
sample population group sex
sample1 sample1 sample1 2
sample2 sample2 sample2 2
-
--haploid2diploid
-
with -h option converts haploid genotypes to homozygous diploid
genotypes. For example, the program will print 0 0 instead of the
default 0 -. This is useful for programs which do not handle haploid
genotypes correctly.
-
--sex FILE
-
output sex column in the sample file. The FILE format is
MaleSample M
FemaleSample F
-
--vcf-ids
-
output VCF IDs instead of "CHROM:POS_REF_ALT" IDs
TSV conversion:
-
--tsv2vcf file
-
convert from TSV (tab-separated values) format (such as generated by
23andMe) to VCF. The input file fields can be tab- or space- delimited
-
-c, --columns list
-
comma-separated list of fields in the input file. In the current
version, the fields CHROM, POS, ID, and AA are expected and
can appear in arbitrary order, columns which should be ignored in the input
file can be indicated by "-".
The AA field lists alleles on the forward reference strand,
for example "CC" or "CT" for diploid genotypes or "C"
for haploid genotypes (sex chromosomes). Insertions and deletions
are not supported yet, missing data can be indicated with "--".
-
-f, --fasta-ref file
-
reference sequence in fasta format. Must be indexed with samtools faidx
-
-s, --samples LIST
-
list of sample names. See Common Options
-
-S, --samples-file FILE
-
file of sample names. See Common Options
Example:
# Convert 23andme results into VCF
bcftools convert -c ID,CHROM,POS,AA -s SampleName -f 23andme-ref.fa --tsv2vcf 23andme.txt -Oz -o out.vcf.gz
bcftools csq [OPTIONS] FILE
Haplotype aware consequence predictor which correctly handles combined
variants such as MNPs split over multiple VCF records, SNPs separated by
an intron (but adjacent in the spliced transcript) or nearby frame-shifting
indels which in combination in fact are not frame-shifting.
The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable
with the -c option). The latter is a bitmask of indexes to INFO/BCSQ, with
interleaved haplotypes. See the usage examples below for using the %TBCSQ
converter in query for extracting a more human readable form from this
bitmask. The construction of the bitmask limits the number of consequences
that can be referenced per sample in the FORMAT/BCSQ tags. By default this is 15, but
if more are required, see the --ncsq option.
The program requires on input a VCF/BCF file, the reference genome in fasta
format (--fasta-ref) and genomic features in the GFF3 format downloadable
from the Ensembl website (--gff-annot), and outputs an annotated VCF/BCF
file. Currently, only Ensembl GFF3 files are supported.
By default, the input VCF should be phased. If phase is unknown, or only
partially known, the --phase option can be used to indicate how to handle
unphased data. Alternatively, haplotype aware calling can be turned off
with the --local-csq option.
If conflicting (overlapping) variants within one haplotype are detected,
a warning will be emitted and predictions will be based on only the first
variant in the analysis.
Symbolic alleles are not supported. They will remain unannotated in the
output VCF and are ignored for the prediction analysis.
-
-c, --custom-tag STRING
-
use this custom tag to store consequences rather than the default BCSQ tag
-
-b, --brief-predictions
-
annotate with abbreviated protein-changing predictions. That is, instead of writing
the whole modified protein sequence with potentially hundreds of aminoacids, only an
abbreviated version such as 25E..329>25G..94 will be written
-
-e, --exclude EXPRESSION
-
exclude sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-f, --fasta-ref FILE
-
reference sequence in fasta format (required)
-
--force
-
run even if some sanity checks fail. Currently the option allows to skip
transcripts in malformatted GFFs with incorrect phase
-
-g, --gff-annot FILE
-
GFF3 annotation file (required), such as ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens.
An example of a minimal working GFF file:
# The program looks for "CDS", "exon", "three_prime_UTR" and "five_prime_UTR" lines,
# looks up their parent transcript (determined from the "Parent=transcript:" attribute),
# the gene (determined from the transcript's "Parent=gene:" attribute), and the biotype
# (the most interesting is "protein_coding").
#
# Attributes required for
# gene lines:
# - ID=gene:<gene_id>
# - biotype=<biotype>
# - Name=<gene_name> [optional]
#
# transcript lines:
# - ID=transcript:<transcript_id>
# - Parent=gene:<gene_id>
# - biotype=<biotype>
#
# other lines (CDS, exon, five_prime_UTR, three_prime_UTR):
# - Parent=transcript:<transcript_id>
#
# Supported biotypes:
# - see the function gff_parse_biotype() in bcftools/csq.c
1 ignored_field gene 21 2148 . - . ID=gene:GeneId;biotype=protein_coding;Name=GeneName
1 ignored_field transcript 21 2148 . - . ID=transcript:TranscriptId;Parent=gene:GeneId;biotype=protein_coding
1 ignored_field three_prime_UTR 21 2054 . - . Parent=transcript:TranscriptId
1 ignored_field exon 21 2148 . - . Parent=transcript:TranscriptId
1 ignored_field CDS 21 2148 . - 1 Parent=transcript:TranscriptId
1 ignored_field five_prime_UTR 210 2148 . - . Parent=transcript:TranscriptId
-
-i, --include EXPRESSION
-
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-l, --local-csq
-
switch off haplotype-aware calling, run localized predictions considering
only one VCF record at a time
-
-n, --ncsq INT
-
maximum number of 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.
-
--no-version
-
see Common Options
-
-o, --output FILE
-
see Common Options
-
-O, --output-type b|t|u|z|v
-
see Common Options. In addition, a custom tab-delimited
plain text output can be printed (t).
-
-p, --phase a|m|r|R|s
how to handle unphased heterozygous genotypes:
-
a
-
take GTs as is, create haplotypes regardless of phase (0/1 → 0|1)
-
m
-
merge all GTs into a single haplotype (0/1 → 1, 1/2 → 1)
-
r
-
require phased GTs, throw an error on unphased heterozygous GTs
-
R
-
create non-reference haplotypes if possible (0/1 → 1|1, 1/2 → 1|2)
-
s
-
skip unphased heterozygous GTs
-
-q, --quiet
-
suppress warning messages
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file FILE
-
see Common Options
-
-s, --samples LIST
-
samples to include or "-" to apply all variants and ignore samples
-
-S, --samples-file FILE
-
see Common Options
-
-t, --targets LIST
-
see Common Options
-
-T, --targets-file FILE
-
see Common Options
Examples:
# Basic usage
bcftools csq -f hs37d5.fa -g Homo_sapiens.GRCh37.82.gff3.gz in.vcf -Ob -o out.bcf
# Extract the translated haplotype consequences. The following TBCSQ variations
# are recognised:
# %TBCSQ .. print consequences in all haplotypes in separate columns
# %TBCSQ{0} .. print the first haplotype only
# %TBCSQ{1} .. print the second haplotype only
# %TBCSQ{*} .. print a list of unique consequences present in either haplotype
bcftools query -f'[%CHROM\t%POS\t%SAMPLE\t%TBCSQ\n]' out.bcf
Examples of BCSQ annotation:
# Two separate VCF records at positions 2:122106101 and 2:122106102
# change the same codon. This UV-induced C>T dinucleotide mutation
# has been annotated fully at the position 2:122106101 with
# - consequence type
# - gene name
# - ensembl transcript ID
# - coding strand (+ fwd, - rev)
# - amino acid position (in the coding strand orientation)
# - list of corresponding VCF variants
# The annotation at the second position gives the position of the full
# annotation
BCSQ=missense|CLASP1|ENST00000545861|-|1174P>1174L|122106101G>A+122106102G>A
BCSQ=@122106101
# A frame-restoring combination of two frameshift insertions C>CG and T>TGG
BCSQ=@46115084
BCSQ=inframe_insertion|COPZ2|ENST00000006101|-|18AGRGP>18AQAGGP|46115072C>CG+46115084T>TGG
# Stop gained variant
BCSQ=stop_gained|C2orf83|ENST00000264387|-|141W>141*|228476140C>T
# The consequence type of a variant downstream from a stop are prefixed with *
BCSQ=*missense|PER3|ENST00000361923|+|1028M>1028T|7890117T>C
bcftools filter [OPTIONS] FILE
Apply fixed-threshold filters.
-
-e, --exclude EXPRESSION
-
exclude sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-g, --SnpGap INT[:'indel',mnp,bnd,other,overlap]
-
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..
-
-G, --IndelGap INT
-
filter clusters of indels separated by INT or fewer base pairs allowing
only one to pass. The following example demonstrates the logic of
--IndelGap 2 applied on a deletion and an insertion:
The second indel is filtered:
012345678901
ref .GT.GT..GT..
del .G-.G-..G-..
And similarly here, the second is filtered:
01 23 456 78
ref .A-.A-..A-..
ins .AT.AT..AT..
-
-i, --include EXPRESSION
-
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-m, --mode [+x]
-
define behaviour at sites with existing FILTER annotations. The default
mode replaces existing filters of failed sites with a new FILTER string
while leaving sites which pass untouched when non-empty and setting to
"PASS" when the FILTER string is absent. The "+" mode appends new FILTER
strings of failed sites instead of replacing them. The "x" mode resets
filters of sites which pass to "PASS". Modes "+" and "x" can both be set.
-
--no-version
-
see Common Options
-
-o, --output FILE
-
see Common Options
-
-O, --output-type b|u|z|v
-
see Common Options
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file file
-
see Common Options
-
-s, --soft-filter STRING|+
-
annotate FILTER column with STRING or, with +, a unique filter name generated
by the program ("Filter%d").
-
-S, --set-GTs .|0
-
set genotypes of failed samples to missing value (.) or reference allele (0)
-
-t, --targets chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-T, --targets-file file
-
see Common Options
-
--threads INT
-
see Common Options
bcftools gtcheck [OPTIONS] [-g genotypes.vcf.gz] query.vcf.gz
Checks sample identity. The program can operate in two modes. If the -g
option is given, the identity of 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.
-
--distinctive-sites NUM[,MEM[,DIR]]
-
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.
-
--dry-run
-
Stop after first record to estimate required time.
-
-e, --error-probability INT
-
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.
If performance is an issue, set to 0 for faster run but less accurate results.
-
-g, --genotypes FILE
-
VCF/BCF file with reference genotypes to compare against
-
-H, --homs-only
-
Homozygous genotypes only, useful with low coverage data (requires -g, --genotypes)
-
--n-matches INT
-
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.
-
--no-HWE-prob
-
Disable calculation of HWE probability to reduce memory requirements with
comparisons between very large number of sample pairs.
-
-p, --pairs LIST
-
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..])
-
-P, --pairs-file FILE
-
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
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
Restrict to comma-separated list of regions, see Common Options
-
*-R, --regions-file' FILE
-
Restrict to regions listed in a file, see Common Options
-s, --samples [qry|gt]:'LIST':
List of query samples or -g samples. If neither -s nor -S are given, all possible sample
pair combinations are compared
-S, --samples-file [qry|gt]:'FILE'
File with the query or -g samples to compare. If neither -s nor -S are given, all possible sample
pair combinations are compared
-
-t, --targets file
-
see Common Options
-
-T, --targets-file file
-
see Common Options
-
-u, --use TAG1[,TAG2]
-
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.
Examples:
# 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 index [OPTIONS] in.bcf|in.vcf.gz
Creates index for bgzip compressed VCF/BCF files for random access. CSI
(coordinate-sorted index) is created by default. The CSI format
supports indexing of chromosomes up to length 2^31. TBI (tabix index)
index files, which support chromosome lengths up to 2^29, can be
created by using the -t/--tbi option or using the tabix program
packaged with htslib. When loading an index file, bcftools will try
the CSI first and then the TBI.
Indexing options:
-
-c, --csi
-
generate CSI-format index for VCF/BCF files [default]
-
-f, --force
-
overwrite index if it already exists
-
-m, --min-shift INT
-
set minimal interval size for CSI indices to 2^INT; default: 14
-
-o, --output FILE
-
output file name. If not set, then the index will be created
using the input file name plus a .csi or .tbi extension
-
-t, --tbi
-
generate TBI-format index for VCF files
-
--threads INT
-
see Common Options
Stats options:
-
-n, --nrecords
-
print the number of records based on the CSI or TBI index files
-
-s, --stats
-
Print per contig stats based on the CSI or TBI index files.
Output format is three tab-delimited columns listing the contig
name, contig length (. if unknown) and number of records for
the contig. Contigs with zero records are not printed.
bcftools isec [OPTIONS] A.vcf.gz B.vcf.gz […]
Creates intersections, unions and complements of VCF files. Depending
on the options, the program can output records from one (or more) files
which have (or do not have) corresponding records with the same position
in the other files.
-
-c, --collapse snps|indels|both|all|some|none
-
see Common Options
-
-C, --complement
-
output positions present only in the first file but missing in the others
-
-e, --exclude -|EXPRESSION
-
exclude sites for which EXPRESSION is true. If -e (or -i)
appears only once, the same filtering expression will be applied to all
input files. Otherwise, -e or -i must be given for each input file.
To indicate that no filtering should be performed on a file, use "-" in
place of EXPRESSION, as shown in the example below.
For valid expressions see EXPRESSIONS.
-
-f, --apply-filters LIST
-
see Common Options
-
-i, --include EXPRESSION
-
include only sites for which EXPRESSION is true. See discussion
of -e, --exclude above.
-
-n, --nfiles [+-=]INT|~BITMAP
-
output positions present in this many (=), this many or more (+), this
many or fewer (-), or the exact same (~) files
-
-o, --output FILE
-
see Common Options. When several files are being
output, their names are controlled via -p instead.
-
-O, --output-type b|u|z|v
-
see Common Options
-
-p, --prefix DIR
-
if given, subset each of the input files accordingly. See also -w.
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file file
-
see Common Options
-
-t, --targets chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-T, --targets-file file
-
see Common Options
-
-w, --write LIST
-
list of input files to output given as 1-based indices. With -p and no
-w, all files are written.
Examples:
Create intersection and complements of two sets saving the output in dir/*
bcftools isec -p dir A.vcf.gz B.vcf.gz
Filter sites in A (require INFO/MAF>=0.01) and B (require INFO/dbSNP) but not in C,
and create an intersection, including only sites which appear in at least two of
the files after filters have been applied
bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e- A.vcf.gz B.vcf.gz C.vcf.gz -n +2 -p dir
Extract and write records from A shared by both A and B using exact allele match
bcftools isec -p dir -n=2 -w1 A.vcf.gz B.vcf.gz
Extract records private to A or B comparing by position only
bcftools isec -p dir -n-1 -c all A.vcf.gz B.vcf.gz
Print a list of records which are present in A and B but not in C and D
bcftools isec -n~1100 -c all A.vcf.gz B.vcf.gz C.vcf.gz D.vcf.gz
bcftools merge [OPTIONS] A.vcf.gz B.vcf.gz […]
Merge multiple VCF/BCF files from non-overlapping sample sets to create one
multi-sample file. For example, when merging file A.vcf.gz containing
samples S1, S2 and S3 and file B.vcf.gz containing samples S3 and
S4, the output file will contain five samples named S1, S2, S3, 2:S3
and S4.
Note that it is responsibility of the user to ensure that the sample names are
unique across all files. If they are not, the program will exit with an error
unless the option --force-samples is given. The sample names can be
also given explicitly using the --print-header and --use-header options.
Note that only records from different files can be merged, never from the same file.
For "vertical" merge take a look at bcftools concat or bcftools norm -m instead.
-
--force-samples
-
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-header
-
print only merged header and exit
-
--use-header FILE
-
use the VCF header in the provided text FILE
-
-0 --missing-to-ref
-
assume genotypes at missing sites are 0/0
-
-f, --apply-filters LIST
-
see Common Options
-
-F, --filter-logic x|+
-
Set the output record to PASS if any of the inputs is PASS (x),
or apply all filters (+), which is the default.
-
-g, --gvcf -|FILE
-
merge gVCF blocks, INFO/END tag is expected. If the reference fasta
file FILE is not given and the dash (-) is given, unknown reference
bases generated at gVCF block splits will be substituted with N’s.
The --gvcf option uses the following default INFO rules:
-i QS:sum,MinDP:min,I16:sum,IDV:max,IMF:max.
-
-i, --info-rules -|TAG:METHOD[,…]
-
Rules for merging INFO fields (scalars or vectors) or - to disable the
default rules. METHOD is one of sum, avg, min, max, join.
Default is DP:sum,DP4:sum if these fields exist in the input files.
Fields with no specified rule will take the value from the first input file.
The merged QUAL value is currently set to the maximum. This behaviour is
not user controllable at the moment.
-
-l, --file-list FILE
-
Read file names from FILE, one file name per line.
-
-L, --local-alleles INT
-
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.
-
-m, --merge snps|indels|both|all|none|id
-
The option controls what types of multiallelic records can be created:
-m none .. no new multiallelics, output multiple records instead
-m snps .. allow multiallelic SNP records
-m indels .. allow multiallelic indel records
-m both .. both SNP and indel records can be multiallelic
-m all .. SNP records can be merged with indel records
-m id .. merge by ID
-
--no-index
-
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.
-
--no-version
-
see Common Options
-
-o, --output FILE
-
see Common Options
-
-O, --output-type b|u|z|v
-
see Common Options
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file file
-
see Common Options
-
--threads INT
-
see Common Options
bcftools mpileup [OPTIONS] -f ref.fa in.bam [in2.bam […]]
Generate VCF or BCF containing genotype likelihoods for one or multiple
alignment (BAM or CRAM) files. This is based on the original
samtools mpileup command (with the -v or -g options) producing
genotype likelihoods in VCF or BCF format, but not the textual pileup
output. The mpileup command was transferred to bcftools in order to
avoid errors resulting from use of incompatible versions of samtools
and bcftools when using in the mpileup+bcftools call pipeline.
Individuals are identified from the SM tags in the @RG header lines. Multiple
individuals can be pooled in one alignment file, also one individual can be
separated into multiple files. If sample identifiers are absent, each input
file is regarded as one sample.
Note that there are two orthogonal ways to specify locations in the
input file; via -r region and -t positions. The
former uses (and requires) an index to do random access while the
latter streams through the file contents filtering out the specified
regions, requiring no index. The two may be used in conjunction. For
example a BED file containing locations of genes in chromosome 20
could be specified using -r 20 -t chr20.bed, meaning that the
index is used to find chromosome 20 and then it is filtered for the
regions listed in the BED file. Also note that the -r option can be much
slower than -t with many regions and can require more memory when
multiple regions and many alignment files are processed.
Input options
-
-6, --illumina1.3+
-
Assume the quality is in the Illumina 1.3+ encoding.
-
-A, --count-orphans
-
Do not skip anomalous read pairs in variant calling.
-
-b, --bam-list FILE
-
List of input alignment files, one file per line [null]
-
-B, --no-BAQ
-
Disable probabilistic realignment for the computation of base alignment
quality (BAQ). BAQ is the Phred-scaled probability of a read base being
misaligned. Applying this option greatly helps to reduce false SNPs caused
by misalignments.
-
-C, --adjust-MQ INT
-
Coefficient for downgrading mapping quality for reads containing
excessive mismatches. Given a read with a phred-scaled probability q of
being generated from the mapped position, the new mapping quality is
about sqrt((INT-q)/INT)*INT. A zero value (the default) disables this functionality.
-
-d, --max-depth INT
-
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]
-
-E, --redo-BAQ
-
Recalculate BAQ on the fly, ignore existing BQ tags
-
-f, --fasta-ref FILE
-
The faidx-indexed reference file in the FASTA format. The file can be
optionally compressed by bgzip. Reference is required by default
unless the --no-reference option is set [null]
-
--no-reference
-
Do not require the --fasta-ref option.
-
-G, --read-groups FILE
-
list of read groups to include or exclude if prefixed with "^".
One read group per line. This file can also be used to assign new sample
names to read groups by giving the new sample name as a second
white-space-separated field, like this: "read_group_id new_sample_name".
If the read group name is not unique, also the bam file name can
be included: "read_group_id file_name sample_name". If all
reads from the alignment file should be treated as a single sample, the
asterisk symbol can be used: "* file_name sample_name". Alignments without
a read group ID can be matched with "?". NOTE: The meaning of bcftools mpileup -G
is the opposite of samtools mpileup -G.
RG_ID_1
RG_ID_2 SAMPLE_A
RG_ID_3 SAMPLE_A
RG_ID_4 SAMPLE_B
RG_ID_5 FILE_1.bam SAMPLE_A
RG_ID_6 FILE_2.bam SAMPLE_A
* FILE_3.bam SAMPLE_C
? FILE_3.bam SAMPLE_D
-
-q, -min-MQ INT
-
Minimum mapping quality for an alignment to be used [0]
-
-Q, --min-BQ INT
-
Minimum base quality for a base to be considered [13]
-
-r, --regions CHR|CHR:POS|CHR:FROM-TO|CHR:FROM-[,…]
-
Only generate mpileup output in given regions. Requires the alignment files
to be indexed. If used in conjunction with -l then considers the intersection;
see Common Options
-
-R, --regions-file FILE
-
As for -r, --regions, but regions read from FILE;
see Common Options
-
--ignore-RG
-
Ignore RG tags. Treat all reads in one alignment file as one sample.
-
--rf, --incl-flags STR|INT
-
Required flags: skip reads with mask bits unset [null]
-
--ff, --excl-flags STR|INT
-
Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]
-
-s, --samples LIST
-
list of sample names. See Common Options
-
-S, --samples-file FILE
-
file of sample names to include or exclude if prefixed with "^".
One sample per line. This file can also be used to rename samples by giving
the new sample name as a second white-space-separated column, like this:
"old_name new_name". If a sample name contains spaces, the spaces can be
escaped using the backslash character, for example "Not\ a\ good\ sample\
name".
-
-t, --targets LIST
-
see Common Options
-
-T, --targets-file FILE
-
see Common Options
-
-x, --ignore-overlaps
-
Disable read-pair overlap detection.
Output options
-
-a, --annotate LIST
-
Comma-separated list of FORMAT and INFO tags to output. (case-insensitive,
the "FORMAT/" prefix is optional, and use "?" to list available annotations
on the command line) [null]:
FORMAT/AD .. Allelic depth (Number=R,Type=Integer)
FORMAT/ADF .. Allelic depths on the forward strand (Number=R,Type=Integer)
FORMAT/ADR .. Allelic depths on the reverse strand (Number=R,Type=Integer)
FORMAT/DP .. Number of high-quality bases (Number=1,Type=Integer)
FORMAT/SP .. Phred-scaled strand bias P-value (Number=1,Type=Integer)
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)
-
-g, --gvcf INT[,…]
-
output gVCF blocks of homozygous REF calls, with depth (DP) ranges
specified by the list of integers. For example, passing 5,15 will
group sites into two types of gVCF blocks, the first with minimum
per-sample DP from the interval [5,15) and the latter with minimum
depth 15 or more. In this example, sites with minimum per-sample
depth less than 5 will be printed as separate records, outside of
gVCF blocks.
-
--no-version
-
see Common Options
-
-o, --output FILE
-
Write output to FILE, rather than the default of standard output.
(The same short option is used for both --open-prob and --output. If -o's
argument contains any non-digit characters other than a leading + or -
sign, it is interpreted as --output. Usually the filename extension
will take care of this, but to write to an entirely numeric filename use -o
./123 or --output 123.)
-
-O, --output-type b|u|z|v
-
see Common Options
-
--threads INT
-
see Common Options
Options for SNP/INDEL genotype likelihood computation
-
-e, --ext-prob INT
-
Phred-scaled gap extension sequencing error probability. Reducing INT
leads to longer indels [20]
-
-F, --gap-frac FLOAT
-
Minimum fraction of gapped reads [0.002]
-
-h, --tandem-qual INT
-
Coefficient for modeling homopolymer errors. Given an l-long homopolymer
run, the sequencing error of an indel of size s is modeled as INT*s/l [100]
-
-I, --skip-indels
-
Do not perform INDEL calling
-
-L, --max-idepth INT
-
Skip INDEL calling if the average per-sample depth is above INT [250]
-
-m, --min-ireads INT
-
Minimum number gapped reads for indel candidates INT [1]
-
-o, --open-prob INT
-
Phred-scaled gap open sequencing error probability. Reducing INT leads
to more indel calls. (The same short option is used for both --open-prob
and --output. When -o’s argument contains only an optional + or - sign
followed by the digits 0 to 9, it is interpreted as --open-prob.) [40]
-
-p, --per-sample-mF
-
Apply -m and -F thresholds per sample to increase sensitivity of calling.
By default both options are applied to reads pooled from all samples.
-
-P, --platforms STR
-
Comma-delimited list of platforms (determined by @RG-PL) from which
indel candidates are obtained. It is recommended to collect indel
candidates from sequencing technologies that have low indel error rate
such as ILLUMINA [all]
Examples:
Call SNPs and short INDELs, then mark low quality sites and sites with the read
depth exceeding a limit. (The read depth should be adjusted to about twice the
average read depth as higher read depths usually indicate problematic regions
which are often enriched for artefacts.) One may consider to add -C50 to
mpileup if mapping quality is overestimated for reads containing excessive
mismatches. Applying this option usually helps for BWA-backtrack alignments,
but may not other aligners.
bcftools mpileup -Ou -f ref.fa aln.bam | \
bcftools call -Ou -mv | \
bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > var.flt.vcf
bcftools norm [OPTIONS] file.vcf.gz
Left-align and normalize indels, check if REF alleles match the reference,
split multiallelic sites into multiple rows; recover multiallelics from
multiple rows. Left-alignment and normalization will only be applied if
the --fasta-ref option is supplied.
-
-a, --atomize
-
Decompose complex variants, e.g. split MNVs into consecutive SNVs.
See also --atom-overlaps and --old-rec-tag.
-
--atom-overlaps .|*
-
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
-
-c, --check-ref e|w|x|s
-
what to do when incorrect or missing REF allele is encountered:
exit (e), warn (w), exclude (x), or set/fix (s) bad sites.
The w option can be combined with x and s. Note that s
can swap alleles and will update genotypes (GT) and AC counts,
but will not attempt to fix PL or other fields. 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.)
-
-d, --rm-dup snps|indels|both|all|exact
-
If a record is present multiple times, output only the first instance.
See also --collapse in Common Options.
-
-D, --remove-duplicates
-
If a record is present in multiple files, output only the first instance.
Alias for -d none, deprecated.
-
-f, --fasta-ref FILE
-
reference sequence. Supplying this option will turn on left-alignment
and normalization, however, see also the --do-not-normalize
option below.
-
--force
-
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-sum TAG[,…]
-
keep vector sum constant when splitting multiallelic sites. Only AD tag
is currently supported. See also https://github.com/samtools/bcftools/issues/360
-
-m, --multiallelics -|+[snps|indels|both|any]
-
split multiallelic sites into biallelic records (-) or join
biallelic sites into multiallelic records (+). An optional type string
can follow which controls variant types which should be split or merged
together: If only SNP records should be split or merged, specify snps; if
both SNPs and indels should be merged separately into two records, specify
both; if SNPs and indels should be merged into a single record, specify
any.
-
--no-version
-
see Common Options
-
-N, --do-not-normalize
-
the -c s option can be used to fix or set the REF allele from the
reference -f. The -N option will not turn on indel normalisation
as the -f option normally implies
-
--old-rec-tag STR
-
Add INFO/STR annotation with the original record. The format of the
annotation is CHROM|POS|REF|ALT|USED_ALT_IDX.
-
-o, --output FILE
-
see Common Options
-
-O, --output-type b|u|z|v
-
see Common Options
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file file
-
see Common Options
-
-s, --strict-filter
-
when merging (-m+), merged site is PASS only if all sites being merged PASS
-
-t, --targets LIST
-
see Common Options
-
-T, --targets-file FILE
-
see Common Options
-
--threads INT
-
see Common Options
-
-w, --site-win INT
-
maximum distance between two records to consider when locally
sorting variants which changed position during the realignment
bcftools [plugin NAME|+NAME] [OPTIONS] FILE — [PLUGIN OPTIONS]
A common framework for various utilities. The plugins can be used
the same way as normal commands only their name is prefixed with "+".
Most plugins accept two types of parameters: general options shared by all
plugins followed by a separator, and a list of plugin-specific options. There
are some exceptions to this rule, some plugins do not accept the common
options and implement their own parameters. Therefore please pay attention to
the usage examples that each plugin comes with.
VCF input options:
-
-e, --exclude EXPRESSION
-
exclude sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-i, --include EXPRESSION
-
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file file
-
see Common Options
-
-t, --targets chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-T, --targets-file file
-
see Common Options
Plugin options:
-
-h, --help
-
list plugin’s options
-
-l, --list-plugins
List all available plugins.
By default, appropriate system directories are searched for installed plugins.
You can override this by setting the BCFTOOLS_PLUGINS environment variable
to a colon-separated list of directories to search.
If BCFTOOLS_PLUGINS begins with a colon, ends with a colon, or contains
adjacent colons, the system directories are also searched at that position
in the list of directories.
-
-v, --verbose
-
print debugging information to debug plugin failure
-
-V, --version
-
print version string and exit
List of plugins coming with the distribution:
-
ad-bias
-
find positions with wildly varying ALT allele frequency (Fisher test on FMT/AD)
-
add-variantkey
-
add VariantKey INFO fields VKX and RSX
-
af-dist
-
collect AF deviation stats and GT probability distribution given AF and assuming HWE
-
allele-length
-
count the frequency of the length of REF, ALT and REF+ALT
-
check-ploidy
-
check if ploidy of samples is consistent for all sites
-
check-sparsity
-
print samples without genotypes in a region or chromosome
-
color-chrs
-
color shared chromosomal segments, requires trio VCF with phased GTs
-
contrast
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
-
counts
-
a minimal plugin which counts number of SNPs, Indels, and total number of sites.
-
dosage
-
print genotype dosage. By default the plugin searches for PL, GL and GT, in
that order.
-
fill-from-fasta
-
fill INFO or REF field based on values in a fasta file
-
fill-tags
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)"
-
fix-ploidy
-
sets correct ploidy
-
fixref
-
determine and fix strand orientation
-
frameshifts
-
annotate frameshift indels
-
GTisec
-
count genotype intersections across all possible sample subsets in a vcf file
-
GTsubset
-
output only sites where the requested samples all exclusively share a genotype
-
guess-ploidy
-
determine sample sex by checking genotype likelihoods (GL,PL) or genotypes (GT)
in the non-PAR region of chrX.
-
gvcfz
-
compress gVCF file by resizing non-variant blocks according to specified criteria
-
impute-info
-
add imputation information metrics to the INFO field based on selected FORMAT tags
-
indel-stats
-
calculates per-sample or de novo indels stats. The usage and format is similar
to smpl-stats and trio-stats
-
isecGT
-
compare two files and set non-identical genotypes to missing
-
mendelian
-
count Mendelian consistent / inconsistent genotypes.
-
missing2ref
-
sets missing genotypes ("./.") to ref allele ("0/0" or "0|0")
-
parental-origin
-
determine parental origin of a CNV region
-
prune
-
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-overlaps
-
remove overlapping variants and duplicate sites
-
scatter
-
intended as an inverse to
bcftools concat
, scatter VCF by chunks or regions, creating multiple VCFs.
-
setGT
-
general tool to set genotypes according to rules requested by the user
-
smpl-stats
-
calculates basic per-sample stats. The usage and format is similar to
indel-stats and trio-stats.
-
split
-
split VCF by sample, creating single- or multi-sample VCFs
-
split-vep
-
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.
-
tag2tag
-
convert between similar tags, such as GL and GP
-
trio-dnm2
-
screen variants for possible de-novo mutations in trios
-
trio-stats
-
calculate transmission rate in trio children. The usage and format is similar to
indel-stats and smpl-stats.
-
trio-switch-rate
-
calculate phase switch rate in trio samples, children samples must have phased GTs
-
variantkey-hex
-
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 path
-
output directory
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file file
-
see Common Options
-
-s, --sample string
-
sample name
-
-t, --targets LIST
-
see Common Options
-
-T, --targets-file FILE
-
see Common Options
-
-v, --verbose
-
verbose debugging output which gives hints about the thresholds and decisions made
by the program. Note that the exact output can change between versions.
Algorithm options:
-
-b, --peak-size float
-
the minimum peak size considered as a good match can be from the interval [0,1]
where larger is stricter
-
-c, --cn-penalty float
-
a penalty for increasing copy number state. How this works: multiple peaks
are always a better fit than a single peak, therefore the program prefers
a single peak (normal copy number) unless the absolute deviation of the
multiple peaks fit is significantly smaller. Here the meaning of
"significant" is given by the float from the interval [0,1] where
larger is stricter.
-
-f, --fit-th float
-
threshold for goodness of fit (normalized absolute deviation), smaller is stricter
-
-i, --include-aa
-
include also the AA peak in CN2 and CN3 evaluation. This usually requires increasing -f.
-
-m, --min-fraction float
-
minimum distinguishable fraction of aberrant cells. The experience shows that trustworthy
are estimates of 20% and more.
-
-p, --peak-symmetry float
-
a heuristics to filter failed fits where the expected peak symmetry is violated.
The float is from the interval [0,1] and larger is stricter
bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz […]]
Extracts fields from VCF or BCF files and outputs them in user-defined format.
-
-e, --exclude EXPRESSION
-
exclude sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-f, --format FORMAT
-
learn by example, see below
-
-H, --print-header
-
print header
-
-i, --include EXPRESSION
-
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-l, --list-samples
-
list sample names and exit
-
-o, --output FILE
-
see Common Options
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file file
-
see Common Options
-
-s, --samples LIST
-
see Common Options
-
-S, --samples-file FILE
-
see Common Options
-
-t, --targets chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-T, --targets-file file
-
see Common Options
-
-u, --allow-undef-tags
-
do not throw an error if there are undefined tags in the format string,
print "." instead
-
-v, --vcf-list FILE
-
process multiple VCFs listed in the file
Format:
%CHROM The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER)
%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.
-
-f, --fai FILE
-
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
-
-h, --header FILE
-
new VCF header
-
-o, --output FILE
-
see Common Options
-
-s, --samples FILE
-
new sample names, one name per line, in the same order as they appear
in the VCF file. Alternatively, only samples which need to be renamed
can be listed as "old_name new_name\n" pairs separated by whitespaces,
each on a separate line. If a sample name contains spaces, the
spaces can be escaped using the backslash character, for example
"Not\ a\ good\ sample\ name".
-
--threads INT
-
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 FLOAT
-
in case allele frequency is not known, use the FLOAT. By default, sites where
allele frequency cannot be determined, or is 0, are skipped.
-
--AF-tag TAG
-
use the specified INFO tag TAG as an allele frequency estimate
instead of the default AC and AN tags. Sites which do not have TAG
will be skipped.
-
--AF-file FILE
-
Read allele frequencies from a tab-delimited file containing
the columns: CHROM\tPOS\tREF,ALT\tAF. The file can be compressed with
bgzip and indexed with tabix -s1 -b2 -e2. Sites which are not present in
the FILE or have different reference or alternate allele will be skipped.
Note that such a file can be easily created from a VCF using:
bcftools query -f'%CHROM\t%POS\t%REF,%ALT\t%INFO/TAG\n' file.vcf | bgzip -c > freqs.tab.gz
-
-b, --buffer-size INT[,INT]
-
when the entire many-sample file cannot fit into memory, a sliding
buffer approach can be used. The first value is the number of sites
to keep in memory. If negative, it is interpreted as the maximum
memory to use, in MB. The second, optional, value sets the number
of overlapping sites. The default overlap is set to roughly 1% of
the buffer size.
-
-e, --estimate-AF FILE
-
estimate the allele frequency by recalculating INFO/AC and INFO/AN on
the fly, using the specified TAG which can be either FORMAT/GT ("GT")
or FORMAT/PL ("PL"). If TAG is not given, "GT" is assumed. Either all
samples ("-") or samples listed in FILE will be included. For example,
use "PL,-" to estimate AF from FORMAT/PL of all samples.
If neither -e nor the other --AF-… options are given, the allele frequency is
estimated from AC and AN counts which are already present in the INFO field.
-
--exclude EXPRESSION
-
exclude sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-G, --GTs-only FLOAT
-
use genotypes (FORMAT/GT fields) ignoring genotype likelihoods (FORMAT/PL),
setting PL of unseen genotypes to FLOAT. Safe value to use is 30 to
account for GT errors.
-
--include EXPRESSION
-
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-I, --skip-indels
-
skip indels as their genotypes are usually enriched for errors
-
-m, --genetic-map FILE
-
genetic map in the format required also by IMPUTE2. Only the first and
third column are used (position and Genetic_Map(cM)). The FILE can
chromosome name.
-
-M, --rec-rate FLOAT
-
constant recombination rate per bp. In combination with --genetic-map,
the --rec-rate parameter is interpreted differently, as FLOAT-fold increase of
transition probabilities, which allows the model to become more sensitive
yet still account for recombination hotspots. Note that also the range
of the values is therefore different in both cases: normally the
parameter will be in the range (1e-3,1e-9) but with --genetic-map
it will be in the range (10,1000).
-
-o, --output FILE
-
Write output to the FILE, by default the output is printed on stdout
-
-O, --output-type s|r[z]
-
Generate per-site output (s) or per-region output (r). By default
both types are printed and the output is uncompressed. Add z for
a compressed output.
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file file
-
see Common Options
-
-s, --samples LIST
-
see Common Options
-
-S, --samples-file FILE
-
see Common Options
-
-t, --targets chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-T, --targets-file file
-
see Common Options
HMM Options:
-
-a, --hw-to-az FLOAT
-
P(AZ|HW) transition probability from AZ (autozygous) to HW (Hardy-Weinberg) state
-
-H, --az-to-hw FLOAT
-
P(HW|AZ) transition probability from HW to AZ state
-
-V, --viterbi-training FLOAT
-
estimate HMM parameters using Baum-Welch algorithm, using the convergence threshold
FLOAT, e.g. 1e-10 (experimental)
bcftools sort [OPTIONS] file.bcf
-
-m, --max-mem FLOAT[kMG]
-
Maximum memory to use. Approximate, affects the number of temporary files written
to the disk. Note that if the command fails at this step because of too many open files,
your system limit on the number of open files ("ulimit") may need to be increased.
-
-o, --output FILE
-
see Common Options
-
-O, --output-type b|u|z|v
-
see Common Options
-
-T, --temp-dir DIR
-
Use this directory to store temporary files
bcftools stats [OPTIONS] A.vcf.gz [B.vcf.gz]
Parses VCF or BCF and produces text file stats which is suitable for machine
processing and can be plotted using plot-vcfstats. When two files are given,
the program generates separate stats for intersection and the complements. By
default only sites are compared, -s/-S must given to include also sample
columns.
When one VCF file is specified on the command line, then stats by non-reference allele
frequency, depth distribution, stats by quality and per-sample counts, singleton stats,
etc. are printed.
When two VCF files are given, then stats such as concordance (Genotype concordance by
non-reference allele frequency, Genotype concordance by sample, Non-Reference Discordance)
and correlation are also printed. Per-site discordance (PSD) is also printed in --verbose mode.
-
--af-bins LIST|FILE
-
comma separated list of allele frequency bins (e.g. 0.1,0.5,1)
or a file listing the allele frequency bins one per line (e.g. 0.1\n0.5\n1)
-
--af-tag TAG
-
allele frequency INFO tag to use for binning. By default the allele frequency is
estimated from AC/AN, if available, or directly from the genotypes (GT) if not.
-
-1, --1st-allele-only
-
consider only the 1st alternate allele at multiallelic sites
-
-c, --collapse snps|indels|both|all|some|none
-
see Common Options
-
-d, --depth INT,INT,INT
-
ranges of depth distribution: min, max, and size of the bin
-
--debug
-
produce verbose per-site and per-sample output
-
-e, --exclude EXPRESSION
-
exclude sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-E, --exons file.gz
-
tab-delimited file with exons for indel frameshifts statistics. The columns
of the file are CHR, FROM, TO, with 1-based, inclusive, positions. The file
is BGZF-compressed and indexed with tabix
tabix -s1 -b2 -e3 file.gz
-
-f, --apply-filters LIST
-
see Common Options
-
-F, --fasta-ref ref.fa
-
faidx indexed reference sequence file to determine INDEL context
-
-i, --include EXPRESSION
-
include only sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-I, --split-by-ID
-
collect stats separately for sites which have the ID column set ("known
sites") or which do not have the ID column set ("novel sites").
-
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-R, --regions-file file
-
see Common Options
-
-s, --samples LIST
-
see Common Options
-
-S, --samples-file FILE
-
see Common Options
-
-t, --targets chr|chr:pos|chr:from-to|chr:from-[,…]
-
see Common Options
-
-T, --targets-file file
-
see Common Options
-
-u, --user-tstv <TAG[:min:max:n]>
-
collect Ts/Tv stats for any tag using the given binning [0:1:100]
-
-v, --verbose
-
produce verbose per-site and per-sample output
bcftools view [OPTIONS] file.vcf.gz [REGION […]]
View, subset and filter VCF or BCF files by position and filtering expression.
Convert between VCF and BCF. Former bcftools subset.
Output options
-
-G, --drop-genotypes
-
drop individual genotype information (after subsetting if -s option is set)
-
-h, --header-only
-
output the VCF header only
-
-H, --no-header
-
suppress the header in VCF output
-
-l, --compression-level [0-9]
-
compression level. 0 stands for uncompressed, 1 for best speed and 9 for
best compression.
-
--no-version
-
see Common Options
-
-O, --output-type b|u|z|v
-
see Common Options
-o, --output FILE:
output file name. If not present, the default is to print to standard output (stdout).
Subset options:
-
-a, --trim-alt-alleles
-
remove 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.
-
--force-samples
-
only warn about unknown subset samples
-
-I, --no-update
-
do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
-
-s, --samples LIST
-
see Common Options. Note that it is possible to create
multiple subsets simultaneously using the split plugin.
-
-S, --samples-file FILE
-
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.
Also note that one must be careful when sample subsetting and filtering is performed in a single command
because the order of internal operations can influence the result. For example, the -i/-e filtering
is performed before sample removal, but the -P filtering is performed after,
and some are inherently ambiguous, for example allele counts can be taken from the INFO
column when present but calculated on the fly when absent. Therefore it is strongly recommended to spell out the
required order explicitly by separating such commands into two steps. (Make sure to use the -O u option
when piping!)
-
-c, --min-ac INT[:nref|:alt1|:minor|:major|:'nonmajor']
-
minimum allele count (INFO/AC) of sites to be printed.
Specifying the type of allele is optional and can be set to
non-reference (nref, the default), 1st alternate (alt1), the least
frequent (minor), the most frequent (major) or sum of all but the
most frequent (nonmajor) alleles.
-
-C, --max-ac INT[:nref|:alt1|:minor|:'major'|:'nonmajor']
-
maximum allele count (INFO/AC) of sites to be printed.
Specifying the type of allele is optional and can be set to
non-reference (nref, the default), 1st alternate (alt1), the least
frequent (minor), the most frequent (major) or sum of all but the
most frequent (nonmajor) alleles.
-
-e, --exclude EXPRESSION
-
exclude sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-f, --apply-filters LIST
-
see Common Options
-
-g, --genotype [^][hom|het|miss]
-
include only sites with one or more homozygous (hom), heterozygous
(het) or missing (miss) genotypes. When prefixed with ^, the logic
is reversed; thus ^het excludes sites with heterozygous genotypes.
-
-i, --include EXPRESSION
-
include sites for which EXPRESSION is true. For valid expressions see
EXPRESSIONS.
-
-k, --known
-
print known sites only (ID column is not ".")
-
-m, --min-alleles INT
-
print sites with at least INT alleles listed in REF and ALT columns
-
-M, --max-alleles INT
-
print sites with at most INT alleles listed in REF and ALT columns.
Use -m2 -M2 -v snps to only view biallelic SNPs.
-
-n, --novel
-
print novel sites only (ID column is ".")
-
-p, --phased
-
print sites where all samples are phased. Haploid genotypes are
considered phased. Missing genotypes considered unphased unless the
phased bit is set.
-
-P, --exclude-phased
-
exclude sites where all samples are phased
-
-q, --min-af FLOAT[:nref|:alt1|:minor|:major|:nonmajor]
-
minimum allele frequency (INFO/AC / INFO/AN) of sites to be printed.
Specifying the type of allele is optional and can be set to
non-reference (nref, the default), 1st alternate (alt1), the least
frequent (minor), the most frequent (major) or sum of all but the
most frequent (nonmajor) alleles.
-
-Q, --max-af FLOAT[:nref|:alt1|:minor|:major|:nonmajor]
-
maximum allele frequency (INFO/AC / INFO/AN) of sites to be printed.
Specifying the type of allele is optional and can be set to
non-reference (nref, the default), 1st alternate (alt1), the least
frequent (minor), the most frequent (major) or sum of all but the
most frequent (nonmajor) alleles.
-
-u, --uncalled
-
print sites without a called genotype
-
-U, --exclude-uncalled
-
exclude sites without a called genotype
-
-v, --types snps|indels|mnps|other
-
comma-separated list of variant types to select. Site is selected if
any of the ALT alleles is of the type requested. Types are determined
by comparing the REF and ALT alleles in the VCF record not INFO tags
like INFO/INDEL or INFO/VT. Use --include to select based on INFO
tags.
-
-V, --exclude-types snps|indels|mnps|ref|bnd|other
-
comma-separated list of variant types to exclude. Site is excluded if
any of the ALT alleles is of the type requested. Types are determined
by comparing the REF and ALT alleles in the VCF record not INFO tags
like INFO/INDEL or INFO/VT. Use --exclude to exclude based on INFO tags.
-
-x, --private
-
print sites where only the subset samples carry an non-reference allele.
Requires --samples or --samples-file.
-
-X, --exclude-private
-
exclude sites where only the subset samples carry an non-reference allele
bcftools help [COMMAND] | bcftools --help [COMMAND]
Display a brief usage message listing the bcftools commands available.
If the name of a command is also given, e.g., bcftools help view, the detailed
usage message for that particular command is displayed.
bcftools [--version|-v]
Display the version numbers and copyright information for bcftools and the
important libraries used by bcftools.
bcftools [--version-only]
Display the full bcftools version number in a machine-readable format.
EXPRESSIONS
These filtering expressions are accepted by most of the commands.
Valid expressions may contain:
numerical constants, string constants, file names (this is currently
supported only to filter by the ID column)
1, 1.0, 1e-4
"String"
@file_name
arithmetic operators
+,*,-,/
comparison operators
== (same as =), >, >=, <=, <, !=
regex operators "~" and its negation "!~". The expressions are case sensitive unless "/i" is added.
INFO/HAYSTACK ~ "needle"
INFO/HAYSTACK ~ "NEEDless/i"
parentheses
(, )
logical operators. See also the examples below and the filtering tutorial
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]
starting with 1.11, the FILTER column can be queried as follows:
FILTER="PASS"
FILTER="A" .. exact match, for example "A;B" does not pass
FILTER!="A" .. exact match, for example "A;B" does pass
FILTER~"A" .. both "A" and "A;B" pass
FILTER!~"A" .. neither "A" nor "A;B" pass
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:
MAX, MIN, AVG, MEAN, MEDIAN, STDEV, SUM, STRLEN, ABS, COUNT
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:
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
Notes:
-
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
Examples:
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.
Shell expansion:
Note that expressions must often be quoted because some characters
have special meaning in the shell.
An example of expression enclosed in single quotes which cause
that the whole expression is passed to the program as intended:
bcftools view -i '%ID!="." & MAF[0]<0.01'
Please refer to the documentation of your shell for details.