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

tsv

meta

:map

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

*.tsv

:file

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

*.tsv

versions_htsnimtools

${task.process}

:string

The name of the process

htsnimtools

:string

The name of the tool

hts_nim_tools | sed -n 's/version: //p'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

htsnimtools

:string

The name of the tool

hts_nim_tools | sed -n 's/version: //p'

:eval

The expression to obtain the version of the tool

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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