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saigegit / SAIGE

Development for SAIGE and SAIGE-GENE(+)
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Saige gwas giving SE == 0 #94

Open akhilpampana opened 1 year ago

akhilpampana commented 1 year ago

Hello,

I have run gwas analysis in ukbiobank and I have noticed some of the variants which have high allele frequencies having standard error as zero and pvalue as zero. I understand the reasoning for the pvalue as zero but I am not understanding what could be the reason for standard error == 0.

Can you please help me out with this?

Thank you so much for your help.

Regards Akhil

akhilpampana commented 1 year ago

Hello, May I know if there is any response on how to proceed with this? Regards Akhil

saigegit commented 1 year ago

Hi Akhil,

Is this observed with the new version 1.1.9? I think we have addressed the very low p-value issue in the recent versions.

Thanks, Wei

akhilpampana commented 1 year ago

Thank you for the response. I have run it in ukbiobank. I am not sure of the version it has.