Description

Count the instances of each SVTYPE observed in each sample in a VCF.

Input

name:type
description
pattern

meta:map

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

]

vcf:file

The VCF file containing structural variants

*.vcf.gz

Output

name:type
description
pattern

counts

meta:map

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

]

*.tsv:file

A tab-delimited file containing the counts of the SV types

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

svtk
MIT

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