Soft clipping?

[Ben Bimber]

Hello,

 

We have been using MOSAIK2 for several years for genotyping of polygeneic gene families like MHC/HLA.  The fact that Mosaik can retain all possible hits for each multi-mapping read is essential for what we are trying to do.  Recently I tried to compare ‘bwa mem –a’ (which should retain all hits), against Mosaik.  In some instances I noticed bwa was returning hits not found by mosaik.  These almost always were due to instances where BWA would soft clip 4-6 bases from one end of the read, while Mosaik would not.  Are there parameters in mosaic that can be used to control clipping behavior?  For our purposes, I slightly more permissive alignment would actually be quite useful.

 

Thank you for any help,

Ben