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How to distinguish between Missing and ReF in gVCF
I have a naive query which might have discussed earlier. I tried to find in the forum but did not succeed.
Consider gVCF files produced for 3 different samples (single-sample variant calling) and genotyping gVCF to VCF generates the list of only variant sites. When it is required to find the shared variants between 3 samples, if one of the sample has no variant at that particular site in the VCF file, how could it be interpreted, Is it missing due to lack of reads or REF?