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The MergeDiscoveryOutput utility merges the results of a parallel discovery run into genome-wide output files.
In addition to merging the main VCF files, this utility will also merge the auxilliary output files (but leave them in the run directory).
-runDirectory <directory>: The run directory where the output files from each partition are stored.
-O <vcf-file>: The location to write the merged output VCF file.
Geraldine Van der Auwera, PhD