Hi all!
After moving from bwa version 0.5.8c to 0.7.10 I discovered differences that look like errors in the newer version: it seems as BWA doesn't perform soft-clipping anymore, resulting in false positive variant calls:
Is that true? I could find parameters to disable soft-clipping, but no parameter to explicitly turn on soft-clipping.
Both version were used with default parameters (both, bwa aln and bwa sampe).
Any help would be appreciated!
Thank you in advance,
Sebastian
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Sebastian •
I just tried version 0.7.12 via bwa-meth with a test dataset that requires soft-clipping from bison and got a lot of soft-clipped alignments...as expected. So at the very least the most recent version works.
Duplicates are
It seems to be another bug, see thread on seqanswers (sorry for cross-posting!)...
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Hello Sebastian!
It appears that your post has been cross-posted to another site: BWA mailing list and SEQanswers.
This is typically not recommended as it runs the risk of annoying people in both communities.
Give Heng Li a chance to reply to your email from yesterday.
Yes you are right, I just wanted to reach some more users...