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:false ]

tumor

:file

tumor sample input BAM file

*.{bam}

tumor_index

:file

tumor sample BAM index file

*.{bam.bai}

normal

:file

normal sample input BAM file

*.{bam}

normal_index

:file

normal sample BAM index file

*.{bam.bai}

target_bed

:file

BED file containing target regions for variant calling

*.{bed}

meta2

:map

Groovy Map containing reference information

fasta

:file

Reference genome FASTA file

*.{fasta}

meta3

:map

Groovy Map containing reference information

fai

:file

Reference genome FASTA index file

*.{fai}

Output

name:type
description
pattern

vcf

meta

:map

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

*.vcf.gz

:file

Gzipped VCF file containing variants

*.{vcf.gz}

versions

versions.yml

: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
Ask a question on Slack Open an issue on GitHub