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Old 02-19-2014, 08:09 AM   #1
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Join Date: Nov 2013
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Default gaps in calculating mapping quality

Hi all,

I am new to this field and I am having trouble figuring out how mapping quality is calculated for gapped alignments. I looked up in the MAQ/BWA paper, and the following webpage
It seems that mapping quality is only defined for un-gapped alignments (from the sum of base qualities of mis-matched bases).

I also dig into the source code of BWA (pairing function in bwape.c and bwa_approx_mapQ function in bwase.c) but the code is either very hard for me to understand or I couldn't find any clue about the treatment of the gaps.

Any help would be extremely appreciated. Thanks.
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alignment, mapping quality

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