Description

Lofreq subcommand to call low frequency variants from alignments

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM input file

*.{bam}

intervals (file)

BED file containing target regions for variant calling

*.{bed}

fasta (file)

The reference fasta file

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

vcf (file)

VCF output file

*.{vcf}
author
Github user bjohnnyd
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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