bcftools

bcftools subcommand [options] [file]

bcftools is a suite of utilities for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. It is part of the SAMtools/HTSlib project and is widely used in bioinformatics for genomic variant analysis.All commands work transparently with both VCF and BCF files, compressed or uncompressed. The tools are designed to work in pipelines, reading from stdin and writing to stdout.

-Ob

Output compressed BCF

Output compressed VCF (bgzipped)

Output uncompressed VCF

Output uncompressed BCF (fastest for piping)

Restrict to comma-separated regions (chr:from-to format), requires an index

Restrict to regions listed in a file (VCF, BED, or tab-delimited)

Restrict to targets, streamed without an index

Restrict to targets listed in a file

Comma-separated list of samples to include (prefix ^ to exclude)

Read the sample list from a file

Number of extra worker threads used for output compression

Automatically index the output (tbi or csi)

Include sites matching filter expression

Exclude sites matching filter expression

Output file name

Variant Calling

mpileup, call

view, merge, concat, sort, index, convert

filter, query, norm

stats, roh, gtcheck

annotate, csq, fill-tags

reheader, isec, head, cnv, polysomy

consensus

plugin (e.g. +split, +scatter, +fill-tags, +setGT)

Use -Ou when piping between bcftools subcommands to avoid unnecessary compression overhead. Indexed files are required for random access and some operations. VCF/BCF files should be sorted by chromosome and position for most operations.

bcftools was developed as part of the SAMtools project, initially created by Heng Li at the Wellcome Sanger Institute. It became a separate project around 2014 with the HTSlib library rewrite, gaining significant functionality for variant analysis.

samtools(1), tabix(1), bgzip(1), vcftools(1)

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