Question: softclip vs mismatch at either end
gravatar for -_-
3.8 years ago by
-_-850 wrote:

I noticed that in my BWA alignments, given a read that is mostly well aligned but with a few bases at the end mismatched, sometimes it's labeled as a mismatch (M), while at other time it's a softclipping (S). What's the deciding factor for mismatch vs soft clipping?

For example, I have seen cases where two 76bp reads are fully aligned except for the first base, yet in one case the first base is a called as a mismatch, but in the second case it's soft clipped. I wonder what are the possible reasons for such difference.

sam alignment • 1.0k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 3.8 years ago by -_-850

since you posted this three months ago: did you come up with some theories/sources?

ADD REPLYlink written 3.5 years ago by michaela_boell70

No, I still have no answer.

ADD REPLYlink written 3.5 years ago by -_-850

I guess, then there is only the "make test files and see what happens" left.

ADD REPLYlink written 3.5 years ago by michaela_boell70
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