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Old 04-01-2016, 03:30 PM   #1
mpj
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Default Limiting variants from WGS to GWAS regions to get more significant cis/trans eQTLs?

Hi,

I have ~60 WGS and RNA-Seq samples which should be sufficient to analyze cis-eQTLs, however not sufficient for the trans-eQTLs. I am wondering would it be reasonable to preselect variants from vcfs that fall into certain genomic regions, as I am really interested in a particular GWAS category. So after selecting lead plus LD GWAS variants or lead GWAS variants plus all variants in some +/- window, and performing Matrix eQTL, the corrected p-values would become more significant as I am performing less tests, thus I would I get more significant cis and trans eQTLs? Is this statistically correct to do?

Thanks
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