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Is there a way to include only variant sites and no-calls in your final vcf. I know during SNP calls you can only emit variants, or only confident sites or all. However is there a way to reduce your vcf in the end to only variant sites (vsqr passed) and places where no calls could be made. So the end vcfs have only variant sites and missing data - and everything that is not listed in the vcf file is reference. I need such a file for merging with other vcf files - so that every position that is not in the vcfs while merging can be called ref.
So far i have called snps with emit-all and done vsqr - I now want to reduce vcfs in size by excluding NO_VARINATION sites (but want to keep information on "missing" sites)