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  • Checking for No-Calls

    Is there a program I can use on my Mac to check my BigY results for no-calls. I'm interested in finding out whether several specific SNPS, which dont appear on my list but do on my closest matches, were no-calls in my test.

    Jim

  • #2
    Odd that no replies have appeared.

    Answer is yes. Excel or any text editor will do.

    You need to download the vcf and bed files. These are
    text files.

    You need the exact location of the SNP. Since you
    are comparing, you should have those.

    Look at the VCF file first. If it has the location,
    that is your answer.

    If not, look at the bed. This is trickier.

    It has things like:
    chrY 2725567 2725575
    chrY 2725576 2725585
    chrY 2725685 2728126
    chrY 2728127 2728129
    chrY 2728130 2728167
    chrY 2728187 2729628

    This means that the computer has made calls
    in the regions:

    2725568 2725575
    2725577 2725585
    2725686 2728126
    2728128 2728129
    2728131 2728167
    2728188 2729628

    notice the difference in the first column! You
    add one to that column to get the areas where there are reads! I.e.

    2725576 and
    2728126 and
    2728130 are single no-calls, and there are
    also some large areas of nocalls.

    If its not in the vcf file and IS listed as a call in the bed, its the reference allele.

    But this is NOT definitive. Definitive is MUCH harder!
    First you get the BAM file from FTDNA .
    Then you need to download a program call IGV
    http://www.broadinstitute.org/software/igv/download
    and learn to use it. Load up your bam file in IGV. You look up a location
    in the viewer and look at the raw data ... you may decide
    that FTDNA's "caller" program was too conservative.
    Actually once you figure out how to use IGV its very very easy. You really should load up several bams at once and
    compare the same location in them.

    I have looked at dozens of markers in dozens of bam files
    and many questions can be answered reliably by
    suspecting a location is either + or - because of
    the suspected phylogeny and looking in the bam.

    Yes, needing to use the bams is a real drag.

    Comment


    • #3
      Originally posted by dtvmcdonald View Post
      If its not in the vcf file and IS listed as a call in the bed, its the reference allele..
      This statement should be qualified with "usually" it's the reference. There are times when you open up the BAM, you'll find there are between 1 and 3 derived reads when the ancestral seems inconsistent with a kit's matches.

      Ultimately, if you want to check no calls you have go to the BAMs as you mentioned.

      Comment

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