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Merging genomic databases from different intervals (GenomicsDBImport)

Hi all. I'm trying to put a large dataset through GenomicsDBImport, but it's not finishing within my cluster's 72 hr kill time. I know I can make this more efficient by running different parts of the genome simultaneously using -L to specify intervals. But I don't see a tool to merge the resulting interval-based genomic databases afterwards. How can I do that? Or can I just direct everything to the same directory? Thanks!

gatk
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written by raf.marcondes • raf.marcondes

I don't think you can merge GenomicDBs.

Instead, you should create the interval-based GenomicsDBImport databases, then genotype each one to give multiple vcfs, then merge the vcfs.

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written by rbagnall rbagnall

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