Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM file
*.{bam}
meta2{:bash}
:map
Groovy Map containing sample information about the reference fasta
e.g. [ id:‘reference’ ]
fasta{:bash}
:file
Reference genome FASTA file
*.{fasta,fa}
Output
name:type
description
pattern
bam{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bam{:bash}
:file
BAM file with indel qualities inserted into it
*.{bam}
versions{:bash}
versions.yml{:bash}
: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
