I have a set of 82 VCFs files, I merged these all into one as a genotype file and a phenotype of five traits as data. I am looking to make a possible association of these data using Mixed linear model. I tried TASSEL in many ways with different parameters. However, I am not getting any potential significant SNPs after multiple correction using FDR and bonferroni.
Please suggest any other software/pipelines, which can be useful for GWAS study.