Avoid mismatch at end of BWA mem alignment

Question

[ndunofficial]

I noticed BWA will occasionally return alignments with a SNP at the first position, e.g.

ATCATAC
TTCATAC

Is there a parameter that can enforce that the alignment is only extended while the score increases? I would like to avoid these

Answer 1

[ndunofficial]

Update - There appears to be aligner bugs that cause this. The API interface is broken (alignments generated through mem_align1), but the command line tools (alignments generated through worker2) seems to work.