Maq Bug
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?
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?
Labels: Aligners, MAQ, SNP calling, Software
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