Description

Converts VCFs containing structural variants to BED format

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

vcf (file)

A VCF file created with a structural variant caller

*.vcf.gz

tbi (file)

The index for the VCF file

*.vcf.gz.tbi

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

bed (file)

The created BED file

*.bed

Tools

svtk
MIT

Utilities for consolidating, filtering, resolving, and annotating structural variants.