View Single Post
Old 06-14-2010, 11:34 AM   #2
Location: Retirement - Not working with bioinformatics anymore.

Join Date: Apr 2010
Posts: 63

I don't recall having seen a SAM file with an H at the beginning of the CIGAR, only at the end. If the H is at the end (or somehow in the middle) then it shouldn't affect the position.

I would guess the position reflects the first base corresponding to the first H, though that may not be true. My reasoning is, if you're not starting from the first H, why even include the hard clipping in the first place? Since hard clipped sequence isn't included in the reported alignment, the only real reason for including it is to indicate the offset from the state position.

That being said, I'm just guessing here. If somebody knows conclusively, go with whatever they tell you.

Good Luck
mrawlins is offline   Reply With Quote