File number limit for GenotypeGVCFs
I'm trying to figure out if I need to run CombineGVCFs before GenotypeGVCFs. The documentation said "One would use this tool when needing to genotype too large a number of individual gVCFs". Is there a ballpark number for "too large a number of individuals"? For example, if I have 1000 individuals, should I use CombineGVCFs first? If so, is there a recommended chuck size? It seems CombineGVCFs does not take nt/nct option and when I tried to combine 600 files it's estimated to take a week.