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  • Calculating allele frequency from VCF file

    Hi Members,
    Please pardon me, if this have been asked previously.

    I find no proper answered thread for this.
    I have VCF file, with all information. And I need to know allele Frequency.

    ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
    ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
    ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
    ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping">
    ##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping">
    ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed. For indels this value only includes reads which confidently support each allele (posterior prob 0.999 or higher that read contains indicated allele vs all other intersecting indel alleles)">

    Got this information from Isaac Variant caller.

    I have information like:

    chr1 108413 rs200678306 T G 321.00 PASS SNVSB=-29.5;SNVHPOL=6;CSQR=ENSR00001516685|regulatory_region_variant GT:GQ: GQX: DP: DPF:AD 0/1:160:160:59:0:22,37


    Is Allele Frequency 22/37

    Please help.
    Bioinformaticscally calm

  • #2
    Please help. Bouncing it.
    Bioinformaticscally calm

    Comment


    • #3
      Someone could help in this issue?

      Comment


      • #4
        Allele freuqnecy calculation formula

        Allele frequency = Alternative_Allele reads (AD) / Total number of reads (DP)

        Comment

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