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  • mpileup multiple samples - individual DP4/AF1 values

    Hi,

    I am calling SNP from multiple individuals using mpileup. I was wondering whether it is possible to get DP4 and AF1 values for each individual? I currently have DP4 and AF1 values for the combined dataset, but would like them for each individual as well.

  • #2
    mpileup multiple samples - individual DP4/AF1 values

    I have the same question. How can we get dp4 values for each individual. I wrote a command for it but it still keeps the main dp4 an dp values inside.

    I am waiting for your reply!

    Comment


    • #3
      DP4 AF1 per sample from mpileup

      Originally posted by catriona View Post
      Hi,

      I am calling SNP from multiple individuals using mpileup. I was wondering whether it is possible to get DP4 and AF1 values for each individual? I currently have DP4 and AF1 values for the combined dataset, but would like them for each individual as well.
      I Catriona,
      your mail was posted a long time ago but today I 'm interested if you found a solution to extract DP4 and AF1 value per sample.

      5iou

      C├ędric

      Comment


      • #4
        mpileup on multiple samples, AF1 is nagative

        Hi

        I have samtools mpileup results for multiple samples. I am getting AF1 value in -ve too. Can somebody please tell, how it is coming?
        example is
        #CHROM POS Parent cov ID REF ALT QUAL FILTER SNP/INDEL DP IDV IMF VDB AF1 RPB G3 HWE AC1 DP4 MQ FQ PV4 EFF-Detailed FORMAT GT PL
        Chr1 172866 218 . A T 999 PASS SNP 1857 0.1071739 1.956035 0.01064 1 695, 938, 5, 11 49 999 0.45, 1, 7.1e-07, 0.31 GT:PLP:SP:GQ 0/0 0, 175, 255
        Chr1 293453 293 . T C 8.94 PASS SNP 2290 0.2161769 -9.319506 0.01935 2 718, 1116, 126, 179 46 9.01 0.49, 8.6e-11, 0, 1 UTR_3_PRIME(MODIFIER||||LOC_Os01g01580|mRNA|CODING|LOC_Os01g01580.1|LOC_Os01g01580.1:exon_1) GT:PLP:SP:GQ 0/0 0, 152, 255
        Chr1 479013 222 . T C 999 PASS SNP 1976 0.2938518 -0.719586 0.02128 0.9787, 4.189e-17, 0.02128 0.00186 2 1106, 674, 28, 7 49 999 0.034, 0.31, 3e-13, 1 INTRON(MODIFIER||||LOC_Os01g01870|mRNA|CODING|LOC_Os01g01870.1|) GT:PLP:SP:GQ 0/0 0, 166, 255

        Thank you

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