GATK: Difference between revisions

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-Also, when using <code>GenomicsDBImport</code>, make sure to have the option <code>--genomicsdb-shared-posixfs-optimizations</code> enabled as it "Allow[s] 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.
+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.
 ===Earlier versions than GATK 4 === <!--T:14-->