Locate A SNP Number of Reads for Variance and References using Pysam

Question

[a_biologist]

Hi guys,

Quick question please. I have a snp with a chromosome number and location and would like to access the bam file for that particular snp in search for read numbers of reference and variance forward and reverse. How would I do that using python module pysam?

Thanks a lot in advance,

best.

[Ram]

Why the pysam restriction, if I may ask?

[a_biologist]

Hi Ram,

Could you please explain to me what do you mean ?

Thanks

[Ram]

Why does the problem need to be solved only using pysam? There has to be some reason to exclude possibly easier solutions that would involve just plain samtools, right?

[a_biologist]

I want to access the original read count numbers of a particular snp within the bam and to be able to compare the read count numbers with the read numbers in the Variant Calling File for that snp.

[Ram]

You might look at compartmentalizing the problem a bit differently: a tool/pipeline-section (I'll call it a segment) to get read counts for a variant, a segment to fetch the read counts from a VCF file given a variant, and a segment to compare these values. That way, you might use the best tool for each task and get your task done with the least programming required.

Disclaimer: This is my reductionist approach, you are free to experiment with others, of course.

[a_biologist]

I am working with python and my project is all based on programming that is why I asked for some illustration of using pysam to get the read numbers.

[Ram]

I see. I was just curious :)

Answer 1

[Ying W]

Look in the pysam documentation at how to use the pileup function