I have a with approx. 6000 SNPs, from a particular chromosomal region of a non-model organism. I know that this region is implicated in regulating multiple phenotypes with a clear dominance hierarchy. I am trying to look at the association of SNPs from this region with different phenotypes and i have no idea what to do. The dataset i have is generated using whole genome sequence data via the GATK standard pipeline. I extracted the region of interest using VCFtools. When i look at the literature, there is a paper which used R package SNPassoc for the kind of analysis i wish to perform. But i did not understand how exactly to feed my vcf data to this package and there are no tutorials. So, i tried plink, as it has extensive tutorials. but when i perform the analysis and look at the P values, it stops making sense. When i look at the SNPs in IGV, i can clearly see the association of a particular allele with phenotype (heterozygous in dominant forms and homozygous in recessive forms), but the p-value does not reflect this. I had tried GWAS using Tassel before with a different data-set and it gave me very significant values. Since my vcf from GATK is incompatible with Tassel ( i have no idea why), i do not know how to proceed. Any help will be appreciated.
