BWA reporting of sequences matching to reverse complement of reference

[MBekritsky]

Hi,

I'm doing this as a sanity check.

I'm using BWA to align simulated reads to a reference genome, and I'm noticing that in the SAM file, when a read maps to the reverse complement, the reported start position is for the 3' end of the original reverse complemented query sequence (the 5' position of the read in the forward strand in the genome). Also, BWA appears to reverse complement the original query sequence and reverse the quality string. Did I get that right? I'm just trying to make sure I thoroughly understand BWA's output.

Thanks!

[dawe]

AFAIK, this is not only BWA, it is a SAM format specification.
See here, page 5 note 7.

d

[MBekritsky]

Thanks dawe!

I've looked at the SAM manual a number of times, but I seem to have always missed that note....