GenomicsDBimport for large sample sizes

[arunbodd]

Is your feature request related to a problem? Please describe.
Yes, the combinegvcfs tool fails to allocate or process large sample sizes.
Describe the solution you'd like
A solution is to use GenomicsDBImport tool from GATK that support >1000sample sizes for genotype VCFs after haplotypecaller

Describe alternatives you've considered
Have considered binning the samples into batches and combining them, but this tool already does that.

Additional context
None

[zmudge3]

Thanks for opening this, Arun. It's something I have on my shortlist to try out and I think it's a good idea. We have done some experimentation with doing the CombineGVCFs step in smaller batches, then merging, and it seems promising. But GenomicsDBImport may work even better.

I'll leave this issue open until I have more to say on that.