Comparing bwa 0.6.2 to bwa 0.5.9 I'm seeing very different behavior around indels. I'm using default options in both cases and as far as I can tell they haven't changed. I'm aligning Illumina paired end 2x80bp reads. For dbSNP indels of just a few nucleotides bwa 0.5.9 aligns them great - perfect matches for entire read length (plus the indel, except when the indel is near the end of the read) but 0.6.2 soft clips a large fraction of the read and then has a very high number of mismatches plus multiple indels in the remaining portion. Any suggestions?
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