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GenomicsDBImport with many intervals

Hi GATK team,

I am running GATK4 GenomicsDBImport to create somatic PON for TCGA whole-exome-data. I wonder if I can split the interval list to as many as possible (I used 1000 pieces from SplitIntervals, and dispatch the 1000 jobs onto a local cluster)? Will such splitting result in an improvement in performance? Will too many intervals potentially cause trouble in the subsequent analysis?

Thanks!

Answers

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