Hi, I am using FAST LMM to do an association study with the following command. ./FaSTLMM.207c/Bin/Linux_MKL/fastlmmc -verboseOutput -bfile xaj_pp -bfilesim xaj_pp -pheno pheno_w_header.txt -covar human_profile_Covariates_fast_LMM.txt -mpheno 50201 -out FAST_LMM_result_10.txt.
I have SNP dataset from 1000 genome comprised of 445 samples with 5 different population. Also I have phenotype data with same population (445 samples) for 50201 phenotypes. After completion of run, the output I get has p values that are associated with Quantitative trait (phenotype) and so many other output columns that I may need or not. I also get an SNP index with position, however the output does not give any index of phenotype which I need to plot the data of -log10p values of snps index with corresponding phenotype index. I am not sure what I am doing wrong, I followed the protocols Fast_LMM manual. Any advice would be greatly appreciated.
Thanks.
