ERROR:005 No candidate SNPs were found

[Nguyễn Trần Thu Trang]

Hi,

I have several runs on FUMA and they all returned with ERROR:005 (no candidate SNPs were found) when there were SNPs passed the genome-wide threshold. I've tried no MAGMA, increasing P (to 1e-05) but it did not work. My job IDs are 199837, 200686. May I know how to trouble shoot this please?

Your help is greatly appreciated!

Best regards,

Trang

[Marijn Schipper]

Dear Trang,

Have you made sure that the variants you input are part of the 1000 genomes EAS reference panel?
When I check a very small subset of your inputted variants they do not seem to be present in the selected reference panel.
Variants which are not part of the reference panel are dropped from the analysis by FUMA.
If the variants you have inputted should be present in the reference panel, then please check whether your provided genomic coordinates are provided as mapped in hg19.
I hope this answers your question, please let me know if I can help you any further.

Cheers,

Marijn

Op dinsdag 16 augustus 2022 om 06:21:37 UTC+2 schreef kacyng...@gmail.com:

[Nguyễn Trần Thu Trang]

Hi Marijn,

I've checked and the coordinates were mapped in hg38. Reducing the input to rsid/p-value solved the issue. Thank you very much for your input!

Best regards,