Entering edit mode
2.5 years ago
godth13teen ▴ 70
Hi, I recently stumble upon some issue related to improperly paired reads. From my understanding, they are marked with SAM Flag 0x2, and they need to suffice those criteria:
- 2 paired reads need to be on the same chromosome.
- 2 paired reads don't map 'too far' from each other. I can understand the first criteria, but how's about the second one? When are 2 reads 'close enough' to be considered as 'properly' paired?
I have searched for the explanation of this problem, but I haven't found one that specified about BWA yet. I also checked BWA man, they didn't mention about the metrics, either.
Thank you very much
it uses the outliers from the fragment-length distribution for a set of reads.
so if the insert size of one pair is out of [mean - std.ev, mean + std.ev] then it's considered as an improper pair, am I right?