I have been trying to get a joint genotype for exome bed region from whole genome gvcf. However, this is really slow and I am not sure if this is the right approach to do it. I have more than 600 samples and this has been running for more than 10 days. Can someone please clarify?
module load java /gatk-184.108.40.206/gatk --java-options "-Xms4G -Xmx32G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" \ GenomicsDBImport \ --genomicsdb-workspace-path /scratch/chr19 \ --batch-size 50 \ -L /scratch/chr19.exome.bed \ --sample-name-map /scratch/AllSamplesGvcfChr19.list \ --reader-threads 16