Description

Convert VCF with structural variations to CytoSure format

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

sv_vcf:file

VCF file with structural variants

*.{vcf,vcf.gz}

meta2:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

coverage_bed:file

Bed file with coverage data

*.bed

meta3:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

cns:file

CN file from CNVkit, not compatible with coverage_bed file

meta4:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

snv_vcf:file

VCF file with SNVs to calculate probe coverage, not compatible with coverage_bed pattern: ”*.{vcf,vcf.gz}”

blacklist_bed:file

Bed file with regions to exclude

*.bed

Output

name:type
description
pattern

cgh

meta:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.cgh:file

SV

in CytoSure format

*.cgh

versions

versions.yml:file

File containing software versions

versions.yml

Tools

vcf2cytosure
MIT

Convert VCF with structural variations to CytoSure format