ERROR：number of total SNPs/var do not equal to number of analyzed SNPs

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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ERROR：number of total SNPs/var do not equal to number of analyzed SNPs #215

Closed wangxuann1995 closed 4 years ago

wangxuann1995 commented 4 years ago

Sir, When I run gemma -bfile 548_M_sex -gk 1 -o M_kinship, the number of total SNPs/var = 800160, but the number of analyzed SNPs = 44487, what should I do for this error? I use PLINK to impute phenotypes and make sure that there is no missing value in phenotype. Thanks for ahead Wangxuan

wangxuann1995 commented 4 years ago

when I add -notsnp the result are followed ## number of analyzed SNPs = 79221

florianecoulmance commented 4 years ago

Hello,

Did you find any answer to your question ? I appear to be in a very similar case and would like to know what are the details/reasons of this low analysed SNPs number. In my case it happens when using the lmm function of GEMMA.

Floriane