Subsetting reads based on Alleles of Heterozygous SNPs

[DuncanSproul]

Hi,

I'm wondering if anyone knows of a way to subset reads overlapping SNPs based on alleles?

So, we have a list of heterozygous SNPs in a sample and reads aligned to the genome. For any given heterozygous SNP I want to pull out those reads that correspond to allele A and those that contain allele B.

Currently, I've used BEDtools to pull out all reads overlapping a SNP and plan to cycle through each in turn. I then want something to go through these reads and call the allele before doing further analysis on each allele individually.

Any ideas?

Thanks

Duncan

[jnhutchinson]

Hi Duncan,

Did you ever find a good way to do this? I'm working with someone that is trying to do something similar (subset reads by sequence at various read positions)

Best,
John