Description

Query a structural variant database, using a vcf file as query

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

in_occs (list)

A list of allele count tags

in_frqs (list)

A list of allele frequency tags

vcf (file)

query vcf file

*.{vcf,vcf.gz}

vcf_dbs (file)

path to a database vcf, or a comma separated list of vcfs

*.{vcf,vcf.gz}

bedpe_dbs (file)

path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of files

*.{bedpe}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’ ]

versions (file)

File containing software versions

versions.yml

out_occs (list)

A list of allele count tags

out_frqs (list)

A list of allele frequency tags

vcf (file)

Annotated output VCF file

*_query.vcf

Tools