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GenomicsDBImport creates tons of files

JCGrenierJCGrenier Montreal, QCMember ✭✭

Hello dear GATK team!

Thanks for all the good work you are doing for the community! That's an awesome toolkit you're providing!
I was working with a reference genome today that was containing thousands of unplaced contigs. This got me into some troubles when I was doing the GenomicsDBimport step, since it was creating ~200k files for every new sample imported.

Did you have any issue with this? This is a problem for me since we are working on a cluster with some quotas about the number of files per user/group.

Thanks a lot for your help!


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