I am analysing Genotyping-by-sequencing data. I have .vcf file as a result. I have 17 individuals with different SNP loci and I have filtered and removed SNP loci with more than 90% missing data. I was wondering if it makes sense to do a MDS analysis to see the distances between these 17 individuals using PLINK, also using the same program I have obtained IBS, and produced a dendrogram using R. Does this make sense? Any suggestions comments or giudeline is appreciated.
P.S. 17 individuals appertain to the same specie but they have been grown in different places.