Not significant SNP in GWAS has probability more that 0.99 in PAINTOR

gkichaev / PAINTOR_V3.0

Fast, integrative fine mapping with functional data

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Not significant SNP in GWAS has probability more that 0.99 in PAINTOR #31

Open gnovikov opened 5 years ago

gnovikov commented 5 years ago

Hi!

I have been using PAINTOR for the locus of about 700 SNPs, and the SNPs that comes up in all maxcausals from 1 to 4 is not significant in my GWAS summary stats (P-value is 0.02757, so not even suggestive). Why would that be?

Thank you in advance for your help!

Ingezz commented 5 years ago

Did you ever figure out why this happened? Seems a bit odd.

rebox36 commented 4 years ago

Hi gnovikov and Ingezz,

Have you succeeded to fixe the issue ? I obtained the same thing for some of my tested loci. I was thinking of testing only SNPs with a certain pvalue limit. Thank you for your help.

rebox36 commented 4 years ago

Hi, Finally by correcting my LD matrix files no more inconsistencies appear. How are constructed your LD matrix files ?