The gemma model choose problem

genetics-statistics / GEMMA

Genome-wide Efficient Mixed Model Association

https://github.com/genetics-statistics/GEMMA

GNU General Public License v3.0

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The gemma model choose problem #253

Closed K-zhangfengwei closed 3 years ago

K-zhangfengwei commented 3 years ago

I perform GWAS analysis of quality traits, coat color. Very good results and now i write the paper. The command I ran is as follows:

gemma-0.98.1-linux-static -bfile 00_population/06_plink_maf0.05/97 -p BO.txt -gk 2 -o BO
cp output/BO.sXX.txt ./
gemma-0.98.1-linux-static -bfile 00_population/06_plink_maf0.05/97 -k BO.sXX.txt -p BO.txt -lmm 1 -n 1 -o BO

why i need produce the -K flie? How to understand it? and Is this method correct?

pjotrp commented 3 years ago

K is for kinship or GRM. It is in the original paper.