Query a structural variant database, using a vcf file as query
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf{:bash}
:file
query vcf file
*.{vcf,vcf.gz}
in_occs{:bash}
:list
A list of allele count tags
in_frqs{:bash}
A list of allele frequency tags
out_occs{:bash}
out_frqs{:bash}
vcf_dbs{:bash}
path to a database vcf, or a comma separated list of vcfs
bedpe_dbs{:bash}
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{:bash}
Annotated output VCF file
*_query.vcf
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
structural variant database software
