The frontline support team will be slow on the forum because we are occupied with a GATK Workshop on March 26th and 27th 2019. We will be back and available to answer questions on the forum on March 28th 2019.
I am currently unsure of how to interpret the output of GenotypeGVCFs when typing my ~600 samples.
Genotype format at a given locus with 2 alternate alleles:
--This is what I am expecting for each sample
Genotype format at another given locus with 2 alternate alleles:
--I really don't understand this
I have written several down-stream scripts which rely on this format being consistent -- why are there so many fields in some of these lines?
I apologize if this is very obvious and documented somewhere, but I have tried searching with no results.