Hi, we are using Illumina Myeloid panel of ~500 amplicons to sequence certain part of exome by Illumina HiSeq. I were doing alignment using bwa mem with default parameters. In some regions the quality of mapping is very poor. In the first case there is lot of mismatches and in the second case there is lot of soft clipping or mismatches at the ends of some reads. Is it possible to somehow force bwa mem to discard these mappings and is it wise? I mean would you set some speciffic parameters to bwa mem mapping to avoid these or are these virtually unavoidable?