DRAGEN gVCF files and joint calling GATK-GenomicsDB

Question

[brunomiwa]

REQUIRED for all errors and issues: a) GATK version used:

4.5

b) Exact command used:

gatk GenomicsDBImport [GVCFS] --geomicsdb-workspace-path test1 --intervals chr20

gatk GenotypeGVCFs -R references/hs38DH.fa -V gendb://test1 -O test1.vcf

c) Entire program log: The tools ran accordingly, but the VCF output after joint had no variants.

My question is: Does gVCF files from DRAGEN can be used for the joint calling using the GenomicsDB workflow?

[DBScan]

I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much faster and easier job.