softclip vs mismatch at either end
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7.5 years ago
-_- ★ 1.1k

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 • 2.0k views
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since you posted this three months ago: did you come up with some theories/sources?

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No, I still have no answer.

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

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