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’]

vcf:file

Input VCF file, must be generated with GRIDSS

*.{vcf,vcf.gz}

meta2:map

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

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

high_conf_sv

meta:map

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

*.high_confidence_somatic.vcf.bgz:file

VCF file including high confidence somatic SVs

*.vcf.bgz

all_sv

meta:map

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

*.all_somatic.vcf.bgz:file

VCF file including all somatic SVs

*.vcf.bgz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

maintainer
Github user kubranarci
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