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}

meta2 (map)

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

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}
maintainers
Github user MarieLataretu
Github user Krannich479
get in touch
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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