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
Groovy Map containing reference information e.g. [ id:‘test2’ ]
fai
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” ]
A gzipped version of the standardized VCF file
versions_svtk
${task.process}
:string
The process the versions were collected from
svtk
The tool name
0.0.20190615
The expression to obtain the version of the tool
versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
