Hello all!
After creating VCF files for each of my samples individually, I compared variants and found that some samples have called tens of thousands more than their genetically identical siblings have. The reason for this is simply coverage (and i'm using RNA-Seq data).
So instead I created gVCF files (is that the right acronym formatting?) for each sample, so now I have information on where I dont have data - Reference, Variant and No data.
When i run GenotypeGVCFs, I get a VCF which I expected to have an ALT column like ".,,A" to express "same as REF", "no data" and "Adenine" for the three input samples, but instead looks exactly like a regular VCF file for a single sample, except there's a PL tag at the end with Phred Probabilities for each of my three samples. Unfortunately, here again a "0" could mean either "same as REF" or "no data".
So my question is: How do I create a table of variants for all samples, but where the distinction is made between no variant and no data.
All the best,
John