Description

Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

Sorted BAM file

*.{bam}

meta2{:bash}

:map

Groovy Map containing sample information about the reference fasta e.g. [ id:‘reference’ ]

fasta{:bash}

:file

Reference genome FASTA file

*.{fasta}

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*.bam{:bash}

:file

Realignment and sorted BAM file

*.{bam}

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
maintainers
Github user MarieLataretu
Github user Krannich479
get in touch
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