Recompute Mapping Quality of Single Reads?

[svos]

Hi all,


is there any way to recompute mapping qualities of single reads? In my case, I want to trim reads after mapping, so I cut sequence and (base calling) qualities appropriately and adjust the CIGAR string. Further, this should (in most cases i guess) lead to an increased mapping quality, as most of the trimmed bases are mismatches.

Can I recompute mapping quality without performing the mapping step again?

Thank you!!

[dpryan]

In general I would say the answer is, "no, you can't". The exception would be if your aligner happens to track where a number of the non-optimal alignments are. Then you could just short-cut things by adjusting each of those alignments and redetermining which is best and what it's score is. This may not be a fool proof method, it will produce wrong results if you do more than minor trimming.

In other words, you're going to need to remap things.

[svos]

Well, thanks for the answer! In general, I'm not expecting major trimming, no.
But BWA aln isn't tracking alternative possibilities of mapping, right?

[dpryan]

Not in its output (at least from what I recall, I don't pretend to be a bwa expert).

[svos]

OK, thanks! I haven't seen anything like that, either...

Further comments are still welcome! ;-) In the meantime, I will try remapping the reads...