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  • wz4
    Junior Member
    • Nov 2013
    • 1
    #1

    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
    Mapping Quality Scores - Genome Analysis Wiki
    http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores

    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.
    Tags: alignment, mapping quality
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