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GATK: Difference between revisions
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===Multicore usage === <!--T:19--> | ===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 | 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 provides <b>some</b> [https://gatk.broadinstitute.org/hc/en-us/articles/360035890591-Spark SPARK commands]: | ||
<!--T:46--> | <!--T:46--> | ||
<blockquote> | <blockquote> | ||
Not all GATK tools use Spark. | * Not all GATK tools use Spark. | ||
<!--T:47--> | <!--T:47--> | ||
Tools that can use Spark generally have a note to that effect in their respective Tool Doc. | * Tools that can use Spark generally have a note to that effect in their respective Tool Doc. | ||
<!--T:48--> | <!--T:48--> | ||
* Some GATK tools exist in distinct Spark-capable and non-Spark-capable versions. | |||
The "sparkified" versions have the suffix <i>Spark</i> at the end of their names. Many of these are still experimental; down the road we plan to consolidate them so that there will be only one version per tool. | The "sparkified" versions have the suffix <i>Spark</i> at the end of their names. Many of these are still experimental; down the road we plan to consolidate them so that there will be only one version per tool. | ||
<!--T:49--> | <!--T:49--> | ||
* Some GATK tools only exist in a Spark-capable version. | |||
Those tools don't have the "Spark" suffix. | Those tools don't have the "Spark" suffix. | ||
</blockquote> | </blockquote> | ||