I have some reads from a targeted capture kit that bwa gives a mapping quality of 0. I know (probably) the reads are mapped correctly because they do indeed map to the captured gene. Also when I blast the 101bp read they only map to then gene they should map to. The problem comes when I go to call variants because GATK will throw out because the mapping quality is so 0, I could try using -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 with the unified genotyper but I don't think this ideal.
What I would really like to do get a more descriptive mapping quality score since I'm pretty sure its mapped correctly. However I cant really find documentation on the web about mapping qualities of 0.
Since my blast only returned 1 position for my 101bp read, I am assuming the mapping quality score doesn't really come from the entire read, I am thinking perhaps the seed is the main driver of the mapping score and the seed must map to multiple locations in the genome but the entire read does not? Does anyone know if I just increase the seed size will that work? Can I even increase the seed size with bwa sampe?
Thanks for the help