Post date: Aug 28, 2014 10:9:31 PM
I ran another set of 3 chains for the BSLMM but only included loci with MAFs > 5%. I am using the integer version of the genotypes. Here is an example.
gemma -g geno_int_timemaC.txt -p pheno_samplesC.txt -a annotation.txt -bslmm 3 -n 1 -o gemoutProbit_int_timemaCmaf5rep2 -rpace 40 -maf 0.05 -w 3000000 -s 6000000