>I came across an interesting bug today, when trying to work with reads aligned by Smith-Waterman (flag = 130), in PET alignments. Indeed, I even filed a Bug Report on it.
The low down on the “bug” or “feature” (I’m not sure which it is yet), is that sequences containing deletions don’t actually show the deletions – they show the straight genomic sequence at that location. The reason that I figure this is a bug instead of by design is because sequences with insertions show the insertion. So why the discrepancy?
Anyhow, the upshot of it is that I’m only able to use 1/2 of the Smith-Waterman alignments maq produces when doing SNP calls in my software. (I can’t trust that the per-base quality scores align to the correct bases with this bug) Since other people are doing SNP calls using MAQ alignments… what are they doing?