Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

tumor{:bash}

:file

tumor sample input BAM file

*.{bam}

tumor_index{:bash}

:file

tumor sample BAM index file

*.{bam.bai}

normal{:bash}

:file

normal sample input BAM file

*.{bam}

normal_index{:bash}

:file

normal sample BAM index file

*.{bam.bai}

target_bed{:bash}

:file

BED file containing target regions for variant calling

*.{bed}

meta2{:bash}

:map

Groovy Map containing reference information

fasta{:bash}

:file

Reference genome FASTA file

*.{fasta}

meta3{:bash}

:map

Groovy Map containing reference information

fai{:bash}

:file

Reference genome FASTA index file

*.{fai}

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

Gzipped VCF file containing variants

*.{vcf.gz}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
maintainers
Github user nevinwu
Github user AitorPeseta
get in touch
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