I have downloaded the GTEx eqtl raw p-value data for one tissue of interest. I have about 100 candidate SNPs (some in LD with one another) for which I'd like to look for eQTL evidence.
I wrote a script to extract all eQTLs reported for the 100 SNPs of interest. Using this data, I'd like to implement a FDR correction (or other method). However, I'm concerned this approach may be too conservative in not accounting for the correlation among the 100 SNPs.
Does anyone have an idea of how I could address this issue? Or if there are any programs/software out there that offers a solution?
I Was thinking of extracting the 1000 Genomes genotype data (~85 individuals from one of the populations of similar background) for the 100 SNPs and using this program to adjust the p-values: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000456#pgen-1000456-g009
Any thoughts are appreciated.