Avoid mismatch at end of BWA mem alignment
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
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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.
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