Input
Name (Type)
Description
Pattern
The input format. Each format needs a seperate parameter to be specified in the args
:
- GEN/SAMPLE file:
--gensample2vcf
- gVCF file:
--gvcf2vcf
- HAP/SAMPLE file:
--hapsample2vcf
- HAP/LEGEND/SAMPLE file:
--haplegendsample2vcf
- TSV file:
--tsv2vcf
*.{gen,sample,g.vcf,hap,legend}{.gz,}
Tools
bcftools
GPL
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.