Mapping quality and XS score
I am currently looking through bam files using igv to manually check if the mutations not called by Mutect2 are really an error or not.
Until now, to filter reads with low quality, I have used only MAPQ > 30 and didn’t consider AS, XS scores.
However, I found some reads that have MAPQ =60, Base quality = 31, AS=96 and XS=81 which to me is difficult to understand what this means….if i should not count these kind of reads.
Would it be okay to only filter reads with MAPQ or should I consider removing reads with high XS score such as AS=90, XS=81 despite high mapping quality to avoid multiple alignment?
I would really appreciate an opinion about this issue !
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