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  • Calling SNPs from segregating populations

    Dear Everyone,
    I am doing NGS of F2 populations.
    But in manual, I saw only for homozygous either parents.
    Anyone know how to call SNPs for parent 1, parent 2 and offspring?
    Thank you very much

  • #2
    Dear All,
    My understand about genotype in VCF format are correct?

    0- allele from reference
    1- For the first allele listed in ALT
    2- For the second allele listed in ALT
    and so on.
    0/1, 1/2, 2/1, 1/0, 2/0 are heterozygous?
    1/1 is homozygous for allele 1 (parent 1)?
    2/2 is homozygous for allele 2 (parent 2)?
    0/0 is homozygous for reference?

    Thank you

    Comment


    • #3
      Basically correct, with the following extension:

      1/1 is homozygous for allele 1 (parent 1, if parent 1 contained the first allele listed in ALT)
      2/2 is homozygous for allele 2 (parent 2, if parent 2 contained the second allele listed in ALT)
      Last edited by sarvidsson; 03-02-2015, 05:25 AM.

      Comment


      • #4
        Thank you very much Sarvidsson.

        Comment


        • #5
          Originally posted by maivantan View Post
          0/1, 1/2, 2/1, 1/0, 2/0 are heterozygous?
          Correct
          1/1 is homozygous for allele 1 (parent 1)?
          2/2 is homozygous for allele 2 (parent 2)?
          There's no guarantee that allele 1 is from parent 1 and 2 is from parent 2 unless your variant caller explicitly states this. Often allele 1 will just be the most frequent, or the alphabetically first.

          0/0 is homozygous for reference?
          Correct

          Comment


          • #6
            I am clear now.
            Thank you very much Dpryan.

            Comment

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