Description

Inserts indel qualities in a BAM file

Input

name:type
description
pattern

meta:map

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

]

bam:file

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,fa}

Output

name:type
description
pattern

bam

meta:map

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

]

*.bam:file

BAM file with indel qualities inserted into it

*.{bam}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

lofreq
MIT

Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file