How many gvcfs can I combine using genomicDBimport (GATK4)?
I am about to start combining low x gvcfs for many individuals (>4K). In the previous pipeline I had the individuals split into cohorts of ~200 and then hierarchically combined within and then across cohorts using combineGVCFs.
I have tried the genomicDBimport on a couple of samples, and I liked it. However, I can't seem to find any information on how many samples I can provide in the sample map. Would I be able to combine them all in one run?
If not, what would be the alternative? Is it possible to do hierarchical merging like with combineGVCFs?
As the sample map requires the sample names next to the paths leading to the gvcfs, I can't figure out if it is possible to merge genomicDBs for multiple cohorts?