Does anyone know of a tool that can output the positions of mismatches for each alignment in a BAM file? I need the coordinates for the mismatch positions within the read as well as the coordinate in the reference sequence to which it aligns. I have found tools that can do one or the other (SAMStat, samtools mpileup, NGSUtils basecall), but they seem to give inconsistent results. Or will I have to extract the information from the CIGAR string or MD tag manually?
Thanks!
Thanks!
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