GATK: Difference between revisions

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 ===Multicore usage === <!--T:19-->
-Most  GATK (>=4) tools are not multicore by default. This means that you should request only one core when calling them. Some tools use threads in some of the computations (e.g. <code>Mutect2</code> has the <code>--native-pair-hmm-threads</code>) and therefore you can require more CPUs (most of them with up to 4 threads) for these computations. GATK4, however, does provide <b>some</b> [https://gatk.broadinstitute.org/hc/en-us/articles/360035890591-Spark SPARK commands]:
+Most  GATK (>=4) tools are not multicore by default. This means that you should request only one core when calling them. Some tools use threads in some of the computations (e.g. <code>Mutect2</code> has the <code>--native-pair-hmm-threads</code>) and therefore you can require more CPUs (most of them with up to 4 threads) for these computations. GATK4, however, does provide <b>some</b> Spark commands<ref> https://gatk.broadinstitute.org/hc/en-us/articles/360035890591-</ref>
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