lofreq indelqual: Insert indel qualities into BAM file (required for indel predictions)

Usage: lofreq indelqual [options] in.bam
Options:
  -u | --uniform INT[,INT]  Add this indel quality uniformly to all bases.
                            Use two comma separated values to specify
                            insertion and deletion quality separately.
                            (clashes with --dindel)
       --dindel             Add Dindel's indel qualities (Illumina specific)
                            (clashes with -u; needs --ref)
  -f | --ref                Reference sequence used for mapping
                            (Only required for --dindel)
  -o | --out FILE           Output BAM file [- = stdout = default]
       --verbose            Be verbose

The preferred way of inserting indel qualities should be via GATK's BQSR (>=2) If that's not possible, use this subcommand.
The command has two modes: 'uniform' and 'dindel':
- 'uniform' will assign a given value uniformly, whereas
- 'dindel' will insert indel qualities based on Dindel (PMID 20980555).
Both will overwrite any existing values.
Do not realign your BAM file afterwards!