NOT identify additional lead SNPs

[paulrhj...@gmail.com]

Hi,

I'd like to use FUMA SNP2Gene to annotate only lead SNPs which have been replicated in a validation sample. To do this, I have prepared a file with the rsids, chr, and pos of the SNPs and deselected the option to identify additional lead SNPs. However, after running this analysis, I get the same results as when I do not deselect the option to identify additional lead SNPs. In addition, when reviewing the parameters (listed under results), I find that addleadSNPs = 1 for both analyses.

Could you check if this option has been implemented correctly?

Many thanks,

Paul Timmers

PhD Precision Medicine

University of Edinburgh

[Kyoko Watanabe]

Hi Paul,

Thank you for your report and I am sorry for this inconvenience.

Indeed, there was a but when converting parameters.

I have fixed and should work fine now.

Again thank you very much for pointing out.

Please feel free to contact me if you have any further questions/problems.

Best,

Kyoko

[paulrhj...@gmail.com]

Hi Kyoko,

Thank you for responding so quickly! I am happy to confirm the problem has been fixed!

I will certainly let you know if I run into any other issues.

Best,

Paul

[aparna....@gmail.com]

Hi Kyoko,

I am still having this issue, and am also not able to change the minimim P-value to define a lead SNP (changing the p-value threshold still tells me there are not lead snps).

Thank you,

Aparna Chibber

[Kyoko Watanabe]

Hi Aparna,

Can you share your jobID?

I'll have a look at your error log.

Best,

Kyoko