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:‘test’, single_end

]

meta2 (map)

Groovy Map containing reference information

meta3 (map)

Groovy Map containing reference information

tumor_bam (file)

tumor sample input BAM file

*.{bam}

tumor_bai (file)

tumor sample BAM index file

*.{bai}

normal_bam (file)

normal sample input BAM file

*.{bam}

normal_bai (file)

normal sample BAM index file

*.{bai}

fasta (file)

Reference genome FASTA file

*.{fasta}

fai (file)

Reference genome FASTA index file

*.{fai}

target_bed (file)

BED file containing target regions for variant calling

*.{bed}

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)

Gzipped VCF file containing variants

*.{vcf.gz}
author
Github user nevinwu
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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