Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

bam (file)

Sorted BAM file

*.{bam}

fasta (file)

Reference genome FASTA file

*.{fasta}

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

bam (file)

Realignment and sorted BAM file

*.{bam}

Tools

lofreq
MIT

A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data