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  • Delly output

    Hi,
    I am new to using Delly, and trying to figure out what it's output means in human terms so that I can write a script to annotate it. Here is an example output of the deletions:

    HWI-ST885:8214D0ACXX:6:1301:8077:53399 81 GL397261 3815017 37 = 3813982 -1134 Library0
    HWI-ST885:8214D0ACXX:6:2108:4240:66697 97 GL397261 3814043 37 = 3815021 1077 Library0
    HWI-ST885:8214D0ACXX:6:1205:15152:6125 81 GL397261 3815026 37 = 3814044 -1081 Library0
    HWI-ST885:8214D0ACXX:6:2105:17871:91060 81 GL397261 3814993 96 = 3814054 -1026 Library0
    ---------------------------------------------
    GL397261 3814154 3814993 839 4 38.2494 >Deletion_xxx_00000031<

    I get the last part after the 4 calls (i.e., after the dashes) which is saying there is a 839 bp log deletion from GL397261 from the 4 calls with an average.mapping quality of 38.2494

    My question is how does it make this decision, it does not make sense to me. Any help would be much appreciated.

  • #2
    Just as a self note, assuming the first call is from 3815017 to 3813982 that is a distance of 1035 so why 1134 it is 99 bp off; in fact they are all off by 99. Maybe something to do with the read length of 100?
    The negative probably means the directionality (makes sense that way).
    of the 4 calls the smallest number (i.e., start point) is 14054 and the largest (i.e., end point) is 3815026. But these are not the start and end points of the call. Rather it is 3814154 (the read length of 100 is added?) and the end point is the smallest of right hand (flipped if there is a neg) which is 3814993.

    All of this said, I am just trying to visualize it to understand it but it does not make sense to my why things are this way.

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