Convert VCF with structural variations to CytoSure format
meta:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
sv_vcf:file
VCF file with structural variants
*.{vcf,vcf.gz}
meta2:map
coverage_bed:file
Bed file with coverage data
*.bed
meta3:map
cns:file
CN file from CNVkit, not compatible with coverage_bed file
meta4:map
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
cgh
*.cgh:file
SV:s in CytoSure format
*.cgh
versions
versions.yml:file
File containing software versions
versions.yml
