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  • #1

    How to get bwa to report one alignment per read or read pair

    I'm using bwa with the parameters 'sampe -n 1 -N 0' to report 1 alignment per read for a paired-end dataset. However, in the output sam file, I see the same forward/reverse pair report twice to different locations:

    HWI:1:X:2:1101:10063:24879 117 chr1 242612515 0 * = 242612515 0
    HWI:1:X:2:1101:10063:24879 153 chr1 242612515 37 91M = 242612515 0
    HWI:1:X:2:1101:10063:24879 163 chr7 14028507 60 100M = 14028669 264
    HWI:1:X:2:1101:10063:24879 83 chr7 14028669 60 39M1D62M = 14028507 -264

    Why would this happen?
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