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  • Variant Call File Completion Varification

    Hello.

    I am just inquiring if whether the VCF conversion processed completely. in my job report it said :


    [bcfview] 100000 sites processed.
    [afs] 0:92071.007 1:4605.800 2:3323.192
    [afs] 0:75428.076 1:4325.300 2:3606.623
    [afs] 0:40896.181 1:2507.646 2:1959.174
    [afs] 0:32411.039 1:1569.609 2:1122.352
    [afs] 0:28658.411 1:1206.773 2:846.816
    [afs] 0:30663.994 1:2180.141 2:1601.864
    [afs] 0:49943.377 1:3061.805 2:2377.817
    [afs] 0:35460.294 1:2423.947 2:1893.759


    Now In other jobs the processes are up to 200000 sites processed. My VCF files are a little smaller than normal and I just want a way to check if I have the entire vcf file processed completely.

    I looked at the "tail Sample.vcf" and it output


    chrY 21154569 . A G 222 . DP=63;VDB=0.0271;AF1=1;AC1=2;DP4=0,0,25,37;MQ=50;FQ=-214 GT:PLP:SP:GQ 1/1:255,187,0:62:0:99
    chrY 21154603 . A C 222 . DP=37;VDB=0.0347;AF1=1;AC1=2;DP4=0,0,13,22;MQ=50;FQ=-132 GT:PLP:SP:GQ 1/1:255,105,0:35:0:99


    and this means that I have sites ranging up to 21154603.

    Not sure how to check the information i processed.

    thank you

    AC

  • #2
    My reads are around 17-20 million reads and I am not sure how this relates to the report that 100,000 sites were processed.

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