search

nmdp-bioinformatics / pipeline

Consensus assembly and allele interpretation pipeline.
GNU Lesser General Public License v3.0
7 stars 7 forks source link

No interpretation for (some) HLA-A*11, *02, and *24 alleles #69

Closed ckennedy-nmdp closed 9 years ago

ckennedy-nmdp commented 9 years ago

The consensus sequence alignments for these alleles have 3 soft-clipped bases at their starts (with corresponding alignment start sites). Other alleles with correct interpretations aren't soft-clipped at the beginning of their alignments. Instead they begin with matches. I think this is the problem.

ckennedy-nmdp commented 9 years ago

I'm going to try to increase the sensitivity of bwa bwasw by decreasing the mismatch penalty.