lofreq alnqual: add base- and indel-alignment qualities (BAQ, IDAQ) to aligned read records

What it does

This tool can compute base- and/or indel-alignment quality scores for aligned reads in SAM/BAM format and store these scores under the custom tags lb (for the base alignment qualities, ai (insertion alignment qualities) and ad (deletion alignment qualities), which it will add to its output BAM.

These tags and their scores can be reused by LoFreq call, which can incorporate them into its model for variant quality calculation.

Do not realign your reads after adding alignment qualities to them since the scores would not be updated in the process!

Notes:

• While LoFreq call can optionally calculate the exact same scores on the fly if needed, having the scores added to the aligned read records is going to save computation time with repeated variant calling from the same input data.
• The base alignment quality scores have the same meaning as in samtools, but are expressed as absolute scores, not as base quality offsets like with the BQ tag generated by samtools.
• ai and ad tags, if requested, will only be added to reads containing insertions/deletions.