BCFtools are meant as a faster replacement for most of the perl VCFTools commands.

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.

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.


To run this software interactively in a Linux environment run the commands:

module load bcftools

Several versions of bcftools may be available, and the versions may be different on different platforms.To list all versions available on the machine, type

module avail bcftools
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