Query a structural variant database, using a vcf file as query
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf
:file
query vcf file
*.{vcf,vcf.gz}
in_occs
:list
A list of allele count tags
in_frqs
A list of allele frequency tags
out_occs
out_frqs
vcf_dbs
path to a database vcf, or a comma separated list of vcfs
bedpe_dbs
path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of files
*.{bedpe}
Groovy Map containing sample information e.g. [ id:‘test’ ]
*_query.vcf
Annotated output VCF file
versions_svdb
${task.process}
:string
The name of the process
svdb
The name of the tool
svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\1/p'
:eval
The expression to obtain the version of the tool
versions
structural variant database software
