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What is the best GWAS tool to use for a very large cohort data (UK Biobank data)?

I'm considering conducting a GWAS analysis using the UK Biobank data, which involves a very large cohort of 500,000 participants. In our lab, we've previously used the Hail software for GWAS analysis. However, when I explore research papers that have conducted GWAS using UK Biobank data, it seems like BOLT-LMM is the more commonly used tool, sometimes SAIGE or regenie.

My question is: I wonder if using Hail is enough for GWAS with a very large cohort, or if it would be better to use tools like BOLT-LMM. What are the pros and cons of these tools?

I don't know much about BOLT-LMM, SAIGE, and regenie except that they can analyze very large cohorts. If using Hail is sufficient, I would like to keep using Hail since it will save the time and effort of installing and learning how to use new tools.

bolt-lmm gwas regenie saige hail
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updated by GenoMax GenoMax • written by lsy9 • lsy9

1 answer

Usually it boils down to trade accuracy for speed. There is a nice comparison of several tools like Regenie, BOLT-LMM and others in this method LDAK-KIV, Regenie, BOLT-LMM

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written by DBScan • DBScan

This post was maked as spam by biostars filter. I have restored it.

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written by GenoMax GenoMax

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