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_lofreq

${task.process}

:string

Process which generated the version

lofreq

:string

Tool name

lofreq version | sed -n '1s/^.* //p'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

Process which generated the version

lofreq

:string

Tool name

lofreq version | sed -n '1s/^.* //p'

:eval

The expression to obtain the version of the tool

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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