Identify independent SNPs in selected genes

[Diana Van Der Plaat]

I am working on a specific pathway with 34 genes, and I would like to identify all independent SNPs in each gene based on a GWAS I did on all the SNPs with in my 34 genes.

I therefore would like to use a p-value higher than the current possible minimum p-value (Minimum P-value of lead SNPs (<)), which is 1e-5.

Could the program be updated to use for example 0.05 as minimum p-value?

[Kyoko Watanabe]

Hi Diana,

The reason why its maximum is set to 1e-5 is because FUMA is not designed to annotate all SNPs in the genome so if there are lots of peaks and set to P=0.05 for example would cost a lots of computation time.

This won't be a problem in your case (since you have limited number of genes) but I cannot change this setting for specific person.

Alternatively, you can use fake P-value for FUMA input, for example you could multiply 1e-5 for P-value of SNPs with P<0.05.

I'm sorry for the inconvenience.

Best,

Kyoko