Sequence mapping region around SNP with allele specificity

Question

[avinash.sahu]

I have a list of SNPs (around 10000) for which I know my sample is heterozygous at those loci. I have .bam that contains ChipSeq experiment for this sample. I want to find the reads those map to regions around the SNPs with allele specificity. For example lets say I have rs1234 I want how many read maps to major allele of the SNP and how many of reads maps to its minor allele. How can I do this?

Answer 1

[Devon Ryan]

The simplest method, given that you already have alignments, would be to simply parse the output of samtools mpileup (just use the -l option with a file listing the SNP positions). You could then parse the output with a small perl/python/whatever script.

If you were starting from scratch, AlleleSeq would be another option (there are likely many more, it's an easy enough tool to write). You might want to read the paper on that anyway to give you an idea on how to calculate significance.