Convert SV calls to a standardized format.
meta:map
Groovy Map containing sample information. Caller can be one of the tools: delly, manta, melt, wham e.g. [ id:‘test’, caller:“delly” ]
input:file
A gzipped VCF file to be standardized
*.vcf.gz
meta2:map
Groovy Map containing reference information e.g. [ id:‘test2’ ]
fai:file
Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)
*.fai
vcf
Groovy Map containing sample information e.g. [ id:‘test’, caller:“delly” ]
*.vcf.gz:file
A gzipped version of the standardized VCF file
versions
versions.yml:file
File containing software versions
versions.yml
Utilities for consolidating, filtering, resolving, and annotating structural variants.
