Dear Biostar's community,
I'm performing GWAS using RADseq. I have 30 samples, my goal is to discriminate these samples using SNP variation.
I've succesfully applied Stacks (http://catchenlab.life.illinois.edu/stacks/) with my data. And I got a vcf file at the end.
1) I've tried a PCA method using Plink and flashPCA but I didn't have so much result. I know that we have to LD prune our dataset before a PCA but I'm not sure about the others filtering method.
Any recommendations about default Missingness per individual, Missingness per marker, MAF, Hardy-Weinberg equilibrium treshold ?
2) Can you recommend other methods than PCA ?