veqtl-mapper in a replication study --perm option
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6.6 years ago
ATCG ▴ 380

Hi, I am trying to use veqtl-mapper in a replication study. In my original population, I found one veqtl and I am using a second population to replicate this finding using the veqtl-SNP and also its LD proxies. My question is, do I need to permute? If not how can veqtl-mapper be run with permuting, my guess is that I set --perm 0 but would like to confirm this. Also, I would like to make sure that the program is not correcting automatically for all the SNPs included in the vcf file, that is that the p-value is an uncorrected p-value. Thank you!

veqtl-mapper permutations replication LD • 1.2k views
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