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This is a VCF manipulation suite from Heng Li, author of samtools. It is included in the samtools package, but is not a series of subcommands under samtools, rather it is an independent set of tools which are activated by its own subcommands unde the main command bcftools.

Note that it was only capable of a few subcommands before version 0.1.2 (i.e. versions 0.1.19 and before). However from 1.2 onwards it has many more new subcommands.

Brief description of subcommands

  • bcftools query, extracts fields from VCF or BCF files and outputs them in user-defined format.


  • When using samtools mpileup, the output can be piped to
bcftools view -cgbu

The bcftools filter capability is one of the new tools from bcftools v1.2