How to combine the interval after GenomicsDBImport
I am trying to build a GenomicsDB database using GenomicsDBImport on 6000 samples. Running on all chromosomes in one go seems to tage many weeks of processing time. If I use small intervals, how do I then combine the different GenomicsDB foldes afterwards? Or is there a different strategy?
I use GATK 4.1.1 and this is my command with all chromosomes that takes forever
gatk --java-options "-Xmx4g -Xms4g" \
--genomicsdb-workspace-path genomicsdb \
--batch-size 50 \
-L all_chromosomes.bed \
--sample-name-map sample_map \