Description

This tools takes a background VCF, such as gnomad, that has full genome (though in some cases, users will instead want whole exome) coverage and uses that as an expectation of variants.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

vcf (file)

The query VCF file

*.{vcf,vcf.gz,bcf}

tbi (file)

The index of the query VCF file

*.{tbi}

meta2 (map)

Groovy Map containing background VCF information
e.g. [ id:'sample1', single_end:false ]

background_vcf (file)

The background VCF file

*.{vcf,vcf.gz,bcf}

background_tbi (file)

The index of the background VCF file

*.{tbi}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

versions (file)

File containing software versions

versions.yml

tsv (file)

A tab-delimited file comparing the variant count of each region in the query VCF and background VCF

*.tsv
maintainer
Github user nvnieuwk
get in touch
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Tools

htsnimtools
MIT

useful command-line tools written to show-case hts-nim

github.com/brentp/hts-nim-tools