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
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
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