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  • CNVnator: The format of cnv result

    I know CNVnator has been used in 1000 Genomes Project. But there is little of material to explain the format of CNV result. Is there anyone know the format of cnv result? For example:
    deletion chr10:6070441-6074520 4080 0.674906 0.00834134 72162.3
    It is very easy to understand the first three column mean, but is there any can explain the rest of column mean?

  • #2
    This is what I got from the author of CNVnator:

    CNV_type coordinates CNV_size normalized_RD p-val1 p-val2

    normalized_RD -- normalized to 1.
    p-val1 -- is calculated using t-test statistics.
    p-val2 -- is from probability of RD values within the region to be in
    the tails of gaussian distribution describing frequencies of RD values in bins.

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    • #3
      Thx bioworker,
      I think it will help me a lot.

      Comment


      • #4
        Do the graphs make any sense? It would be great if any of you can explain it to me.

        I graphed the below region and here is what I get:
        Code:
        duplication chr1:172376901-172381900	5000	10.2	2.54996e-10	2.65008e-29

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        • #5
          So is there any rules should be used to filter the results based on p-val1 or p-val2? Or all the output on screen are candicate?

          Comment


          • #6
            same question: how to filter result, and which p-val should be considered?

            Comment


            • #7
              same doubt - how to filter the CNVs.
              Maybe p-value of <0.01 or <0.05
              And about the size of CNVs?

              Comment

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