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count number of A,C,G,T using DP4 in VCF



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  • count number of A,C,G,T using DP4 in VCF

    Not sure about DP4 format in VCF of A,C,G,T count
    chr1 90119 . T G,A,X 99 . DP=121;AF1=1;CI95=1,1;DP4=0,7,33,81;MQ=51;PV4=0.19,1,1,0.064 PL 255,208,255,255,0,255,255,255,255,255

    Which one is correct? (Total DP=121= 7+33+81 seems okay.)
    T is 7, G is 33 , A is 81 , C is 0
    T is 7, A is 33 , G is 81, C is 0
    T is 77, forward A/G is 33, reverse A/G is 81, C is 0

    How about this one?
    chr4 1808445 . C T,G,A 99 . DP=459;AF1=1;CI95=1,1;DP4=33,55,260,108;MQ=31;PV4=1.3e-08,3.1e-44,1,4.3e
    -05 PL 186,164,255,255,0,255,255,255,255,255
    I guess: C=33+55, but how many T,G,A ?? Help please.


    According to http://samtools.sourceforge.net/mpileup.shtml

    DP4 is:
    Number of 1) forward ref alleles; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref alleles, used in variant calling. Sum can be smaller than DP because low-quality bases are not counted.
    Last edited by gcrdb; 03-23-2011, 11:32 AM.

  • #2
    Could you answer this question? I have also similar question?


    • #3
      T is 7, forward A/G is 33, reverse A/G is 81, C is 0

      I don't think there is any way of knowing how many G's and A's from DP4, because these are both lumped under 'non-reference'. Have a look at that position in the alignment using tview to confirm this.

      If someone knows of a way to obtain this information from mpileup I would also be very interested to know, as it would be hard to call the right SNP at this location without it.


      • #4
        Did anyone have any luck finding an answer to this?



        • #5
          Did anyone have any luck finding an answer to this?



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