Question: No soft-clipping in BWA 0.7.10 anymore?
0
gravatar for Sebastian
5.2 years ago by
Sebastian10
Germany
Sebastian10 wrote:

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

bwa mapping soft clipping • 2.1k views
ADD COMMENTlink modified 5.2 years ago by Peter5.8k • written 5.2 years ago by Sebastian10

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 REPLYlink modified 5.2 years ago • written 5.2 years ago by Devon Ryan94k

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

ADD REPLYlink written 5.2 years ago by Devon Ryan94k

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

ADD REPLYlink written 5.2 years ago by Sebastian10
1
gravatar for Devon Ryan
5.2 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

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 COMMENTlink written 5.2 years ago by Devon Ryan94k
0
gravatar for Peter
5.2 years ago by
Peter5.8k
Scotland, UK
Peter5.8k wrote:

Duplicates are

ADD COMMENTlink modified 5 months ago by RamRS26k • written 5.2 years ago by Peter5.8k

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

ADD REPLYlink written 5.2 years ago by Sebastian10
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