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{:bash}

:map

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

vcf{:bash}

:file

The query VCF file

*.{vcf,vcf.gz,bcf}

tbi{:bash}

:file

The index of the query VCF file

*.{tbi}

meta2{:bash}

:map

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

background_vcf{:bash}

:file

The background VCF file

*.{vcf,vcf.gz,bcf}

background_tbi{:bash}

:file

The index of the background VCF file

*.{tbi}

Output

name:type
description
pattern

tsv{:bash}

meta{:bash}

:map

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

*.tsv{:bash}

:file

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

*.tsv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

htsnimtools
MIT

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

github.com/brentp/hts-nim-tools
maintainer
Github user nvnieuwk
get in touch
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