Convert SV calls to a standardized format.
meta{:bash}
:map
Groovy Map containing sample information. Caller can be one of the tools: delly, manta, melt, wham e.g. [ id:‘test’, caller:“delly” ]
input{:bash}
:file
A gzipped VCF file to be standardized
*.vcf.gz
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘test2’ ]
fai{:bash}
Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)
*.fai
vcf{:bash}
Groovy Map containing sample information e.g. [ id:‘test’, caller:“delly” ]
*.vcf.gz{:bash}
A gzipped version of the standardized VCF file
versions_svtk{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
svtk{:bash}
The tool name
0.0.20190615{:bash}
The expression to obtain the version of the tool
versions{:bash}
Utilities for consolidating, filtering, resolving, and annotating structural variants.
