Hi all!
I'm using BWA aln (v 0.7.10) to map short reads (75bp - 100bp) to hg19 genome. Is it possible to adjust the penalty for soft-clipping? I want to set it lower than mismatch penalty in order to prevent mismatches at read ends and to favor soft-clipping.
Alternatively, I could increase mismatch penalty, but what is the penalty for soft-clipping?
Thanks for your help!
I'm using BWA aln (v 0.7.10) to map short reads (75bp - 100bp) to hg19 genome. Is it possible to adjust the penalty for soft-clipping? I want to set it lower than mismatch penalty in order to prevent mismatches at read ends and to favor soft-clipping.
Alternatively, I could increase mismatch penalty, but what is the penalty for soft-clipping?
Thanks for your help!
Comment