I got my annotated variants in file1.vcf(control) and file2.vcf(clown) and now I need to find which non-synonymous SNPs are different between Sample Control and sample Clown. which command of vcftools I can use?
1st command merges the 2 samples
2nd splits multeallic records that may appear during the emerging process
3rd selects records where only 1 sample is bearing alternative allele (het or hom)
Just as a recommandation, it is better if you can, to call your 2 samples together. Indeed, if you have a record in one file but none in the other at the same location, you have no way of knowing if this is because second sampes if hom ref at this location or if it is just a no call due to a technical issue.