Description

It predicts variants using multiple processors

Input

name:type
description
pattern

meta:map

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

bam:file

Tumor sample sorted BAM file

*.{bam}

bai:file

BAM index file

*.{bam.bai}

intervals:file

BED file containing target regions for variant calling

*.{bed}

meta2:map

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

fasta:file

Reference genome FASTA file

*.{fasta}

meta3:map

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

fai:file

Reference genome FASTA index file

*.{fai}

Output

name:type
description
pattern

vcf

meta:map

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

]

*.vcf.gz:file

Predicted variants file

*.{vcf}

tbi

meta:map

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

]

*.vcf.gz.tbi:file

Index of vcf file

*.{vcf.gz.tbi}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

lofreq
MIT

Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's call-parallel programme predicts variants using multiple processors

csb5.github.io/lofreq 10.1093/nar/gks918
maintainers
Github user kaurravneet4123
Github user bjohnnyd
Github user nevinwu
Github user AitorPeseta
get in touch
Ask a question on Slack Open an issue on GitHub