GATK: Difference between revisions

Also, when using <code>GenomicsDBImport</code>, make sure to have the option <code>--genomicsdb-shared-posixfs-optimizations</code> enabled as it will [https://gatk.broadinstitute.org/hc/en-us/articles/4414594350619-SelectVariants#--genomicsdb-shared-posixfs-optimizations Allow for optimizations to improve the usability and performance for shared Posix Filesystems(e.g. NFS, Lustre)]. If not possible or if you are using GNU parallel to run multiple intervals at the same time, please copy your database to <code>${SLURM_TMPDIR}</code> and run it from there as your IO operations might disrupt the filesystem. <code>${SLURM_TMPDIR}</code> is a local storage and therefore is not only faster, but the IO operations would not affect other users.