cross-ref CHT output to peaks about wasp HOT 1 CLOSED

Using proximal SNPs as test SNPs is fine as long as the SNPs are close
enough that the haplotypes are accurate. The input files for the CHT
include the target coordinates and the output should be in that same
order. It might be easiest for now to match lines.

On Mon, Oct 10, 2016 at 3:13 PM, Sasha Gusev [email protected]
wrote:

Thanks for putting together such a detailed pipeline description, it was
really helpful in getting everything working.

I ran the CHT using SNPs that were inside and proximal to ChIP-seq peaks
(I assume the haplotypes of heterozygous carriers of proximal SNPs are
tested for imbalance). This means some SNPs get tested twice for multiple
peaks. However, the CHT output only lists the test SNP position and not the
target peak that it was tested for. Am I screwing something up by testing
proximal SNPs? Is there a way to connect the CHT output back to the
corresponding peak positions?

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