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removing low-quality reads by MuTect
Before variant calling, MuTect removes low-quality reads first, please look at short read preprocessing at nature.com/nbt/journal/v31/n3/extref/nbt.2514-S1.pdf. I want to use this short read pre-processing method for my BAM files, and tried to program by perl. But I have no idea about how to program these sentences: (c) if there is an overlapping read pair, and both reads agree the read with the highest quality score is retained otherwise both are discarded. (b) if there is an overlapping read pair, and both reads agree the read with the highest quality score is retained otherwise the read that disagrees with the reference is retained. Can anybody help me to understand them? Thanks very much for help!