I am doing a GWA study on pigs particularly bred for meat What are the data filtering approaches that can be used in GWAS study for these highly selected farm animals ? I know that filtering on HWE and PPC tests in plink will not be valid for these type of data with non random mating. For phenotype filtering I am doing and IBM based clustering in plink, then mds scaling in R , and then I filter out those samples for which the scaling values do not reach a certain threshold (say I filter on absolute value >0.01 ). Is this a valid approach? or are there any other valid approaches?
I appreciate your help.