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GATK: Difference between revisions
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Most GATK (>=4) tools are not multicore by default. This means that you should request only one core when calling these kind of tools. 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 '''some''' [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 these kind of tools. 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 '''some''' [https://gatk.broadinstitute.org/hc/en-us/articles/360035890591-Spark SPARK commands]: | ||
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Not all GATK tools use Spark. | Not all GATK tools use Spark. | ||
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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. | ||
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- Some GATK tools exist in distinct Spark-capable and non-Spark-capable versions. | - Some GATK tools exist in distinct Spark-capable and non-Spark-capable versions. | ||
The "sparkified" versions have the suffix "Spark" 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 "Spark" 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. | ||
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- Some GATK tools only exist in a Spark-capable version. | - 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. | ||