Inserts indel qualities in a BAM file
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam
BAM file
*.{bam}
meta2
Groovy Map containing sample information about the reference fasta e.g. [ id:‘reference’ ]
fasta
Reference genome FASTA file
*.{fasta,fa}
versions
File containing software versions
versions.yml
BAM file with indel qualities inserted into it
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
