bcftools (1) - Linux Man Pages
bcftools: utilities for variant calling and manipulating VCFs and BCFs.
NAME
bcftools - utilities for variant calling and manipulating VCFs and BCFs.
SYNOPSIS
bcftools [--version|--version-only] [--help] [COMMAND] [OPTIONS]
DESCRIPTION
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations. In general, whenever multiple VCFs are read simultaneously, they must be indexed and therefore also compressed. (Note that files with non-standard index names can be accessed as e.g. "bcftools view -r X:2928329 file.vcf.gz##idx##non-standard-index-name".)
BCFtools is designed to work on a stream. It regards an input file "-" as the standard input (stdin) and outputs to the standard output (stdout). Several commands can thus be combined with Unix pipes.
VERSION
This manual page was last updated 2020-11-25 16:08 GMT and refers to bcftools git version 1.11-24-g9718479+.
BCF1
The BCF1 format output by versions of samtools <= 0.1.19 is not compatible with this version of bcftools. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0.1.19 to convert to VCF, which can then be read by this version of bcftools.
-
samtools-0.1.19/bcftools/bcftools view file.bcf1 | bcftools view
VARIANT CALLING
See bcftools call for variant calling from the output of the samtools mpileup command. In versions of samtools <= 0.1.19 calling was done with bcftools view. Users are now required to choose between the old samtools calling model (-c/--consensus-caller) and the new multiallelic calling model (-m/--multiallelic-caller). The multiallelic calling model is recommended for most tasks.
LIST OF COMMANDS
For a full list of available commands, run bcftools without arguments. For a full list of available options, run bcftools COMMAND without arguments.
-
•
annotate .. edit VCF files, add or remove annotations
-
•
call .. SNP/indel calling (former "view")
-
•
cnv .. Copy Number Variation caller
-
•
concat .. concatenate VCF/BCF files from the same set of samples
-
•
consensus .. create consensus sequence by applying VCF variants
-
•
convert .. convert VCF/BCF to other formats and back
-
•
csq .. haplotype aware consequence caller
-
•
filter .. filter VCF/BCF files using fixed thresholds
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•
gtcheck .. check sample concordance, detect sample swaps and contamination
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•
index .. index VCF/BCF
-
•
isec .. intersections of VCF/BCF files
-
•
merge .. merge VCF/BCF files files from non-overlapping sample sets
-
•
mpileup .. multi-way pileup producing genotype likelihoods
-
•
norm .. normalize indels
-
•
plugin .. run user-defined plugin
-
•
polysomy .. detect contaminations and whole-chromosome aberrations
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•
query .. transform VCF/BCF into user-defined formats
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•
reheader .. modify VCF/BCF header, change sample names
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•
roh .. identify runs of homo/auto-zygosity
-
•
sort .. sort VCF/BCF files
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•
stats .. produce VCF/BCF stats (former vcfcheck)
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•
view .. subset, filter and convert VCF and BCF files
LIST OF SCRIPTS
Some helper scripts are bundled with the bcftools code.
-
•
plot-vcfstats .. plots the output of stats
COMMANDS AND OPTIONS
Common Options
The following options are common to many bcftools commands. See usage for specific commands to see if they apply.
FILE
- Files can be both VCF or BCF, uncompressed or BGZF-compressed. The file "-" is interpreted as standard input. Some tools may require tabix- or CSI-indexed files.
-c, --collapse snps|indels|both|all|some|none|id
-
Controls how to treat records with duplicate positions and defines compatible records across multiple input files. Here by "compatible" we mean records which should be considered as identical by the tools. For example, when performing line intersections, the desire may be to consider as identical all sites with matching positions (bcftools isec -c
all), or only sites with matching variant type (bcftools isec -c
snps
-c
indels), or only sites with all alleles identical (bcftools isec -c
none).
none
- only records with identical REF and ALT alleles are compatible
some
- only records where some subset of ALT alleles match are compatible
all
- all records are compatible, regardless of whether the ALT alleles match or not. In the case of records with the same position, only the first will be considered and appear on output.
snps
- any SNP records are compatible, regardless of whether the ALT alleles match or not. For duplicate positions, only the first SNP record will be considered and appear on output.
indels
- all indel records are compatible, regardless of whether the REF and ALT alleles match or not. For duplicate positions, only the first indel record will be considered and appear on output.
both
- abbreviation of "-c indels -c snps"
id
- only records with identical ID column are compatible. Supported by bcftools merge only.
-f, --apply-filters LIST
- Skip sites where FILTER column does not contain any of the strings listed in LIST. For example, to include only sites which have no filters set, use -f .,PASS.
--no-version
- Do not append version and command line information to the output VCF header.
-o, --output FILE
- When output consists of a single stream, write it to FILE rather than to standard output, where it is written by default.
-O, --output-type b|u|z|v
- Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF (v). Use the -Ou option when piping between bcftools subcommands to speed up performance by removing unnecessary compression/decompression and VCF←→BCF conversion.
-r, --regions chr|chr:pos|chr: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.
--no-version
-o, --output FILE
-O, --output-type b|u|z|v
--ploidy ASSEMBLY[?]
--ploidy-file FILE
File format options:
X 1 60000 M 1
X 2699521 154931043 M 1
Y 1 59373566 M 1
Y 1 59373566 F 0
MT 1 16569 M 1
MT 1 16569 F 1
* * * M 2
* * * F 2
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
- see Common Options
-R, --regions-file file
- see Common Options
-s, --samples LIST
- see Common Options
-S, --samples-file FILE
- see Common Options
-t, --targets LIST
- see Common Options
-T, --targets-file FILE
- see Common Options
--threads INT
- see Common Options
-A, --keep-alts
-f, --format-fields list
-F, --prior-freqs AN,AC
Input/output options:
# 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
-c, --consensus-caller
-C, --constrain alleles|trio
alleles
trio
-m, --multiallelic-caller
-n, --novel-rate float[,...]
-p, --pval-threshold float
-P, --prior float
-t, --targets file|chr|chr:pos|chr:from-to|chr:from-[,...]
-X, --chromosome-X
-Y, --chromosome-Y
Consensus/variant calling options:
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).
-c, --control-sample string
-f, --AF-file file
-o, --output-dir path
-p, --plot-threshold float
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
-R, --regions-file file
-s, --query-sample string
-t, --targets LIST
-T, --targets-file FILE
-a, --aberrant float[,float]
-b, --BAF-weight float
-d, --BAF-dev float[,float]
-e, --err-prob float
-l, --LRR-weight float
-L, --LRR-smooth-win int
-O, --optimize float
-P, --same-prob float
-x, --xy-prob float
General Options:
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|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)
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
-m, --mask FILE
- BED file or TAB file with regions to be replaced with N. See discussion of --regions-file in Common Options for file format details.
-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
-e, --exclude EXPRESSION
-i, --include EXPRESSION
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
-R, --regions-file FILE
-s, --samples LIST
-S, --samples-file FILE
-t, --targets LIST
-T, --targets-file FILE
--no-version
-o, --output FILE
-O, --output-type b|u|z|v
--threads INT
-G, --gensample2vcf prefix or gen-file,sample-file
-g, --gensample prefix or gen-file,sample-file
VCF input options:
.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
--gvcf2vcf
-f, --fasta-ref file
--hapsample2vcf prefix or hap-file,sample-file
gVCF conversion:
.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
-H, --haplegendsample2vcf prefix or hap-file,legend-file,sample-file
-h, --haplegendsample prefix or hap-file,legend-file,sample-file
HAP/LEGEND/SAMPLE conversion:
.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
--tsv2vcf file
-c, --columns list
-f, --fasta-ref file
-s, --samples LIST
-S, --samples-file FILE
Example:
TSV conversion:
# 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 in the FORMAT/BCSQ tags. By default this is 16, but if more are required, see the --ncsq option.
The program requires on input a VCF/BCF file, the reference genome in fasta format (--fasta-ref) and genomic features in the GFF3 format downloadable from the Ensembl website (--gff-annot), and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3 files are supported.
By default, the input VCF should be phased. If phase is unknown, or only partially known, the --phase option can be used to indicate how to handle unphased data. Alternatively, haplotype aware calling can be turned off with the --local-csq option.
If conflicting (overlapping) variants within one haplotype are detected, a warning will be emitted and predictions will be based on only the first variant in the analysis.
Symbolic alleles are not supported. They will remain unannotated in the output VCF and are ignored for the prediction analysis.
-c, --custom-tag STRING
- use this custom tag to store consequences rather than the default BCSQ tag
-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 consequences to consider per site. The INFO/BCSQ column includes all consequences, but only the first INT will be referenced by the FORMAT/BCSQ fields. The default value is 16 which corresponds to one integer per diploid sample. Note that increasing the value leads to increased memory and is rarely necessary.
--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.
-c, --csi
-f, --force
-m, --min-shift INT
-o, --output FILE
-t, --tbi
--threads INT
-n, --nrecords
-s, --stats
Indexing options:
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.
Create intersection and complements of two sets saving the output in dir/*
Examples:
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 four samples named S1, S2, S3, 2:S3 and S4.
Note that it is responsibility of the user to ensure that the sample names are unique across all files. If they are not, the program will exit with an error unless the option --force-samples is given. The sample names can be also given explicitly using the --print-header and --use-header options.
Note that only records from different files can be merged, never from the same file. For "vertical" merge take a look at bcftools 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.
-6, --illumina1.3+
-A, --count-orphans
-b, --bam-list FILE
-B, --no-BAQ
-C, --adjust-MQ INT
-d, --max-depth INT
-E, --redo-BAQ
-f, --fasta-ref FILE
--no-reference
-G, --read-groups FILE
Input options
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.
-a, --annotate LIST
Output options
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
-e, --ext-prob INT
-F, --gap-frac FLOAT
-h, --tandem-qual INT
-I, --skip-indels
-L, --max-idepth INT
-m, --min-ireads INT
-o, --open-prob INT
-p, --per-sample-mF
-P, --platforms STR
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.
Options for SNP/INDEL genotype likelihood computation
bcftools mpileup -Ou -f ref.fa aln.bam | \
bcftools call -Ou -mv | \
bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > var.flt.vcf
bcftools norm [OPTIONS] file.vcf.gz
Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows. Left-alignment and normalization will only be applied if the --fasta-ref option is supplied.
-c, --check-ref e|w|x|s
- what to do when incorrect or missing REF allele is encountered: exit (e), warn (w), exclude (x), or set/fix (s) bad sites. The w option can be combined with x and s. Note that s can swap alleles and will update genotypes (GT) and AC counts, but will not attempt to fix PL or other fields. 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
-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.
-e, --exclude EXPRESSION
-i, --include EXPRESSION
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
-R, --regions-file file
-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
-T, --targets-file file
--no-version
-o, --output FILE
-O, --output-type b|u|z|v
--threads INT
-h, --help
-l, --list-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
-V, --version
ad-bias
add-variantkey
af-dist
allele-length
check-ploidy
check-sparsity
color-chrs
contrast
counts
dosage
fill-from-fasta
fill-tags
fix-ploidy
fixref
frameshifts
GTisec
GTsubset
guess-ploidy
gvcfz
impute-info
indel-stats
isecGT
mendelian
missing2ref
parental-origin
prune
remove-overlaps
scatter
setGT
smpl-stats
split
split-vep
tag2tag
trio-dnm
trio-stats
trio-switch-rate
variantkey-hex
VCF input options:
# 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
Things to check if your plugin does not show up in the bcftools plugin -l output:
Plugins troubleshooting:
// 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.
-o, --output-dir path
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
-R, --regions-file file
-s, --sample string
-t, --targets LIST
-T, --targets-file FILE
-v, --verbose
-b, --peak-size float
-c, --cn-penalty float
-f, --fit-th float
-i, --include-aa
-m, --min-fraction float
-p, --peak-symmetry float
General options:
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}]
--AF-dflt FLOAT
--AF-tag TAG
--AF-file FILE
General Options:
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
-a, --hw-to-az FLOAT
-H, --az-to-hw FLOAT
-V, --viterbi-training FLOAT
HMM Options:
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.
-G, --drop-genotypes
-h, --header-only
-H, --no-header
-l, --compression-level [0-9]
--no-version
-O, --output-type b|u|z|v
-o, --output FILE: output file name. If not present, the default is to print to standard output (stdout).
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,...]
-R, --regions-file file
-t, --targets chr|chr:pos|chr:from-to|chr:from-[,...]
-T, --targets-file file
--threads INT
-a, --trim-alt-alleles
--force-samples
-I, --no-update
-s, --samples LIST
-S, --samples-file FILE
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']
-C, --max-ac INT[:nref|:alt1|:minor|:'major'|:'nonmajor']
-e, --exclude EXPRESSION
-f, --apply-filters LIST
-g, --genotype [^][hom|het|miss]
-i, --include EXPRESSION
-k, --known
-m, --min-alleles INT
-M, --max-alleles INT
-n, --novel
-p, --phased
-P, --exclude-phased
-q, --min-af FLOAT[:nref|:alt1|:minor|:major|:nonmajor]
-Q, --max-af FLOAT[:nref|:alt1|:minor|:major|:nonmajor]
-u, --uncalled
-U, --exclude-uncalled
-v, --types snps|indels|mnps|other
-V, --exclude-types snps|indels|mnps|ref|bnd|other
-x, --private
-X, --exclude-private
Output options
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 (".|.", "./.", ".") using these expressions
-
GT~"\.", GT!~"\."
-
-
•
missing genotypes can be matched including the phase and ploidy (".|.", "./.", ".") using these expressions
-
GT=".|.", GT="./.", GT="."
-
-
•
sample genotype: reference (haploid or diploid), alternate (hom or het, haploid or diploid), missing genotype, homozygous, heterozygous, haploid, ref-ref hom, alt-alt hom, ref-alt het, alt-alt het, haploid ref, haploid alt (case-insensitive)
-
GT="ref" GT="alt" GT="mis" GT="hom" GT="het" GT="hap" GT="RR" GT="AA" GT="RA" or GT="AR" GT="Aa" or GT="aA" GT="R" GT="A"
-
-
•
TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,bnd,other,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
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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:
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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:
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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)
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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
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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:
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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:
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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
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MIN(DP)>10 & MIN(DV)>3
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FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
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FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
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QUAL>10 | FMT/GQ>10 .. true for sites with QUAL>10 or a sample with GQ>10, but selects only samples with GQ>10
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QUAL>10 || FMT/GQ>10 .. true for sites with QUAL>10 or a sample with GQ>10, plus selects all samples at such sites
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TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
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COUNT(GT="hom")=0 .. no homozygous genotypes at the site
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AVG(GQ)>50 .. average (arithmetic mean) of genotype qualities bigger than 50
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ID=@file .. selects lines with ID present in the file
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ID!=@~/file .. skip lines with ID present in the ~/file
-
MAF[0]<0.05 .. select rare variants at 5% cutoff
-
POS>=100 .. restrict your range query, e.g. 20:100-200 to strictly sites with POS in that range.
Shell expansion:
Note that expressions must often be quoted because some characters have special meaning in the shell. An example of expression enclosed in single quotes which cause that the whole expression is passed to the program as intended:
-
bcftools view -i '%ID!="." & MAF[0]<0.01'
Please refer to the documentation of your shell for details.
SCRIPTS AND OPTIONS
plot-vcfstats [OPTIONS] file.vchk [...]
Script for processing output of bcftools stats. It can merge results from multiple outputs (useful when running the stats for each chromosome separately), plots graphs and creates a PDF presentation.
-m, --merge
- Merge vcfstats files to STDOUT, skip plotting.
-p, --prefix DIR
- The output directory. This directory will be created if it does not exist.
-P, --no-PDF
- Skip the PDF creation step.
-r, --rasterize
- Rasterize PDF images for faster rendering. This is the default and the opposite of -v, --vectors.
-s, --sample-names
- Use sample names for xticks rather than numeric IDs.
-t, --title STRING
- Identify files by these titles in plots. The option can be given multiple times, for each ID in the bcftools stats output. If not present, the script will use abbreviated source file names for the titles.
-v, --vectors
- Generate vector graphics for PDF images, the opposite of -r, --rasterize.
-T, --main-title STRING
- Main title for the PDF.
Example:
-
# Generate the stats bcftools stats -s - > file.vchk
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# Plot the stats plot-vcfstats -p outdir file.vchk
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# The final looks can be customized by editing the generated # 'outdir/plot.py' script and re-running manually cd outdir && python plot.py && pdflatex summary.tex
PERFORMANCE
HTSlib was designed with BCF format in mind. When parsing VCF files, all records are internally converted into BCF representation. Simple operations, like removing a single column from a VCF file, can be therefore done much faster with standard UNIX commands, such as awk or cut. Therefore it is recommended to use BCF as input/output format whenever possible to avoid large overhead of the VCF → BCF → VCF conversion.
BUGS
Please report any bugs you encounter on the github website: http://github.com/samtools/bcftools
AUTHORS
Heng Li from the Sanger Institute wrote the original C version of htslib, samtools and bcftools. Bob Handsaker from the Broad Institute implemented the BGZF library. Petr Danecek, Shane McCarthy and John Marshall are maintaining and further developing bcftools. Many other people contributed to the program and to the file format specifications, both directly and indirectly by providing patches, testing and reporting bugs. We thank them all.
RESOURCES
BCFtools GitHub website: http://github.com/samtools/bcftools
Samtools GitHub website: http://github.com/samtools/samtools
HTSlib GitHub website: http://github.com/samtools/htslib
File format specifications: http://samtools.github.io/hts-specs
BCFtools documentation: http://samtools.github.io/bcftools
BCFtools wiki page: https://github.com/samtools/bcftools/wiki
COPYING
The MIT/Expat License or GPL License, see the LICENSE document for details. Copyright (c) Genome Research Ltd.