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./. V.S. 0/0 when using CombineVariants

Dear GATK team,

I noticed that when using CombineVariants on vcf files containing different sets of samples, snps which are not harbored by all vcfs and all samples would be marked as ./. in the combined vcf for the samples which didn't contain those snps in the original vcf.

However if the samples in the original vcf didn't harbor those snps, it is possible that those SNPs are the same as references, other than ./. which means uncalled, and should be marked as 0/0 instead in the combined vcf. Is there a way can do this?


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