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Hi,
There is a problem that comes with me when I try to understand how bwa-mem calculates the AS score.
I'm running BWA MEM (0.7.17-r1188) on paired-end reads with default parameters. I know that in default a match is 1, a mismatch is -4, a gap opening is -6, and a gap extension is -1.
However, in this read, It seems Read1 does not match this score calculation method. It has 148 alignment matches in CIGAR(which contain matches and mismatches), and from NM tag and MD tag we can know that there are 17 mismatches in this alignment, then its alignment score should be (148-17)-17*4, but it has an AS of 66, I don't know where the extra 3 points came from.
Hi,
There is a problem that comes with me when I try to understand how bwa-mem calculates the AS score.
I'm running BWA MEM (0.7.17-r1188) on paired-end reads with default parameters. I know that in default a match is 1, a mismatch is -4, a gap opening is -6, and a gap extension is -1.
However, in this read, It seems Read1 does not match this score calculation method. It has 148 alignment matches in CIGAR(which contain matches and mismatches), and from NM tag and MD tag we can know that there are 17 mismatches in this alignment, then its alignment score should be (148-17)-17*4, but it has an AS of 66, I don't know where the extra 3 points came from.
Does anyone have any insight into why this might be the case?
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