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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

vcf (file)

Predicted variants file

*.{vcf}
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

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