No soft-clipping in BWA 0.7.10 anymore?
2
0
Entering edit mode
7.5 years ago
Sebastian ▴ 10

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

Mapping soft-clipping BWA • 3.0k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Give Heng Li a chance to reply to your email from yesterday.

ADD REPLY
0
Entering edit mode

Yes you are right, I just wanted to reach some more users...

ADD REPLY
1
Entering edit mode
7.5 years ago

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.

ADD COMMENT
0
Entering edit mode
7.5 years ago
Peter 6.0k

Duplicates are

ADD COMMENT
0
Entering edit mode

It seems to be another bug, see thread on seqanswers (sorry for cross-posting!)...

ADD REPLY

Login before adding your answer.

Traffic: 1291 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6