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jianyangqt / gcta

GCTA software
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Rare Variant in Spare GRM #11

Closed Shicheng-Guo closed 2 years ago

Shicheng-Guo commented 2 years ago

Dear Prof. Yang,

I am wondering do we have any evaluation on how rare variants affect Spare GRM? should we include rare variants in GRM calculation?

Thanks

Shicheng

longmanz commented 2 years ago

Hi Shicheng,

In a standard GWAS analysis with GCTA-fastGWA, we recommend users to remove any variants with MAF < 0.01 when calculating the sparse GRM. Sparse GRM in fastGWA is used to model/approach the pedigree structure of the samples, while including rare variants would somehow "inflate" the genetic relationship coefficients between individuals.

Best, Longda

jianyangqt commented 2 years ago

Dear Shicheng,

We don’t need many genetic variants to track the segregation of chromosome segments in a pedigree with a few generations. So, using the common variants will be sufficient. Including a large number of rare variants in the GRM computation will increase the variance in the estimated genetic relatedness (as indicated by Longda), which is proportional to the effective number of independent markers.

Best regards, Jian

Professor Jian Yang School of Life Sciences, Westlake University, Hangzhou Zhejiang 310024 China. T: +86-571-87089837. W: Lab websitehttps://yanglab.westlake.edu.cn/

From: Shicheng Guo @.> Reply-To: jianyangqt/gcta @.> Date: Thursday, February 3, 2022 at 7:51 AM To: jianyangqt/gcta @.> Cc: Subscribed @.> Subject: [jianyangqt/gcta] Rare Variant in Spare GRM (Issue #11)

Dear Prof. Yang,

I am wondering do we have any evaluation on how rare variants affect Spare GRM? should we include rare variants in GRM calculation?

Thanks

Shicheng

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