Description

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

Input

Name (Type)
Description
Pattern

meta (map)

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

meta2 (map)

Groovy Map containing information for PONDIR
e.g. [ id:‘test’]

vcf (file)

Input VCF file, must be generated with GRIDSS

*.{vcf,vcf.gz}

pondir (directory)

Directory containing Panel Of Normal bed/bedpe used to filter FP somatic events. Use gridss.GeneratePonBedpe to generate the PON.

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

high_conf_sv (file)

VCF file including high confidence somatic SVs

*.vcf.bgz

all_sv (file)

VCF file including all somatic SVs

*.vcf.bgz