Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

VCF input file

*.{vcf}

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.gz{:bash}

:file

VCF filtered output file

*.{vcf}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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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