Description

Lofreq subcommand to remove variants with low coverage or strand bias potential

Input

name:type
description
pattern

meta

:map

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

vcf

:file

VCF input file

*.{vcf}

Output

name:type
description
pattern

vcf

meta

:map

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

*.gz

:file

VCF filtered output file

*.{vcf}

versions_lofreq

${task.process}

:string

Process which generated the version

lofreq

:string

Tool name

lofreq version | sed -n '1s/^.* //p'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

Process which generated the version

lofreq

:string

Tool name

lofreq version | sed -n '1s/^.* //p'

:eval

The expression to obtain the version of the tool

Tools

lofreq
MIT

A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data

csb5.github.io/lofreq csb5.github.io/lofreq/commands 10.1093/nar/gks918
included in
tbanalyzer
maintainer
Github user bjohnnyd
get in touch
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