GWAS - need software that outputs effect size and se or variance

Question

[mcsimenc]

Hi all,

I am working on a GWAS, and need to get p-value, effect size or odds ratio, and standard error/deviation or variance for each SNP. I want these stats because I want to calculate bayes factors (SP-EBF: https://doi.org/10.1038/s41431-020-00800-x).

I ran PyGWAS but of these it only outputs p-value. I want to try GAPIT using MLM model as I know it can output these but I do not have enough memory available. I'm working with about 126Gb RAM + 120Gb swap and a large VCF file. Anyone know of another GWAS pipeline I can run to get these outputs and will work with my memory constraint?

Thanks so much

[Helix]

There are several GWAS tools which can produce the outputs that you want based on LMM models. Some of which are REGENIE, BOLT-LMM, fast-GWA and SAIGE. Among these, REGENIE is the most computational efficient one. Hope this helps.