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  • Find SNP in 454HCDiffs.txt

    Hey there,

    I mapped my reads against a reference consisting of the isotigs of the de novo assembly of the same reads. I'm wondering now if the follwoing approach is really sufficient to detect SNPs in the 454HCDiff.txt:
    - get the summary line of each diff: grep '>' 454HCDiffs.txt
    - check if the start and end position are identical (SNPs need to be at the same position in the reference)
    - check if neither the ref nucleotide nor the var nucleotide is only a gap

    - check if the var nucleotide length is 1

    Regards,
    Thomas
    Last edited by dschika; 01-18-2011, 03:46 AM.

  • #2
    Yes, that approach will give you a list of putative SNP/SNVs.

    But you will want to do further filtering (e.g. on read depth, quality) to get a more trusted set of SNPs.

    Comment


    • #3
      Thanks for your quick reply!

      I thought it would be sufficient to take the 454HCDiffs.txt file, because of the High Confidence. That means that (please see the manual for full details):
      - there must be at least 3 non-duplicate reads with the difference
      - there must be forward and reverse reads with the difference, unless there are at least 5 reads with quality score over 20

      Do you think that those filtering options are still too smooth? Can you perhaps suggest some other values?

      Btw: I added another step in my first post.

      Comment


      • #4
        It will depend on a number of factors. For example if you have greater coverage then you might want to set the read depth cut-off higher. It will depend also on the quality of your reference genome - that might have errors in it. You need to take a view depending on what you are trying to do.

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