BCFTools

BCFTools is a suit of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. The tool is designed for handling data streams and as such treats input / output files as stdin and stdout. Therefore when passing multiple files they must be properly indexed and compressed.

This suit consists of the following commands:

Command	Description
`annotate`	add or remove annotations of a VCF
`call`	SNP/indel calling
`cnv`	Copy number variation caller
`concat`	concatenate VCF/BCF files from the same set of samples
`consensus`	create a consensus sequence by applying VCF variants
`convert`	convert VCF to BCF and vise versa
`csq`	haplotype aware consequence caller
`filter`	filter VCF/BCF files using fixed thresholds
`gtcheck`	check sample concordance, detect sample swaps and contamination
`head`	view file headers
`index`	index files
`isec`	intersections of files
`merge`	merge 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
`query`	transform files into user-defined formats
`reheader`	modify header and change sample names
`roh`	identify runs of homo/auto-zygosity utilizing a HMM.
`sort`	sort files
`stats`	produce stats and can be visualized with `plot-vcfstats`
`view`	subset, filter, and convert files

Two additional scripts are bundled with bcftools and they are gff2gff and plot-vcfstats. gff2gff converts a GFF file to the format required by csq while plot-vcfstats plots the output of stats.

For additional information please see the documentation

ml biocontainers bcftools
bcftools stats -s <stdin> > file.vchk
plot-vcfstats -p outdir file.vchk
cat in.gff.gz | gff2gff | gzip -c > out.gff.gz

Parallel Capabilities: Single core only.