how to differentiate b/n a no-call and a homozygous-for-the-REF

Question

[Ephremephraim]

Dear All:I am trying to merge several individual vcfs. While using vcftools to merge them: error-columns don't match. So I concerted each file into a plink file and then merged them (I may add, after so many --exclude of several truly triallelic sites!!....is there a way to avoid this exclusion..flipping is no good here). But then, how do I easily differentiate b/n a true 'no-call' and a true 'homozygous-for-the-REF' in the merged single plink file.....which both appear as '00'. Please help me as soon as you can....I am stuck. BTW: I am doing a case-control association study. Desperately, Ephraim.

[Pierre Lindenbaum]

see Back-filling missing genotypes in merged VCF