I'm having issues trying to run a multivariate linear mixed model (lmm) Genome Wide Association Study (GWAS).
My input files & genotyping files are fine, but when I tried to run the GWAS in Gemma, the program stalled.
I've no issue running GWAS on individual phenotypes, but I've been told that a multivariate analysis using Gemma won't work; because my input phenotype values are biomodal & apparently Gemma can only run multivariate GWAS on data with a normal distribution.
Here is the input I used on Gemma:
gemma -bfile multivariate_genotypes -k output/kinship.cXX.txt -n 2 3 -lmm -o multivate_PC1+PC2_lmm_20JUN2017
Please let me know if I'm using Gemma incorrectly or if you can suggest more appropriate software.