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  • Pysam pileup working unpredictably

    Hi,

    I'm trying to count allelic frequencies at SNPs and Pysam seems to be the best solution to do that. However, when I make a call to get the number of reads that occur at a single site I get many more sites than expected.

    Example:
    len(list(f.pileup(reference='chr1',start=1756880,end=1756881)))

    gives a result of 135 as opposed to the expected value of 1

    and

    len(list(f.pileup(reference='chr1',start=1756870,end=1756881)))

    gives a result of 146 as opposed to 10.

    Can anyone please explain what is going on?

    Regards,

    P. Korir

  • #2
    I suspect that pileup givess you pileups for every base covered by a read that was within the query range.

    edit: You might want to print the pos of each PileupColumn. for p in f.pileup(...): print p.pos, p.n ...

    Comment


    • #3
      Thanks for your reply ffinkernagel.

      Well, I'm surprised that when I give it a query range of 1 it gives more than one result. Anyway, I have used the for loop like in your suggestion though the solution is not as clean as I wanted it to be.

      f.pileup() returns an iterator. I'm not proficient in the use of iterators.

      P. Korir

      Comment


      • #4
        you simply do
        for something in my_iterator:
        do_something_with(something)

        no difference to a list there.

        The for loop should tell you if my hunch is correct.

        Comment


        • #5
          OK. I'll give it a shot.

          Thank you.

          Comment

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