I used BWA to map my PE sequencing data to reference genome. I try to use paired mapping quality to filter bad read pairs out for downstream analysis.
How BWA calculate paired mapping quality? I understand it calculates single-end mapping quality like MAQ does. But I am not sure how it proceeds after having the single mapping quality for both ends? Simply add up or something more complicated? I’ve checked the source code, but the program does not make much sense without a good understanding of the variable names/notations. FYI, the relevant source code is located in the ‘static int pairing’ function of the bwape.c file.
I would really appreciate your input.
pparg
How BWA calculate paired mapping quality? I understand it calculates single-end mapping quality like MAQ does. But I am not sure how it proceeds after having the single mapping quality for both ends? Simply add up or something more complicated? I’ve checked the source code, but the program does not make much sense without a good understanding of the variable names/notations. FYI, the relevant source code is located in the ‘static int pairing’ function of the bwape.c file.
I would really appreciate your input.
pparg
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