GATK: Difference between revisions

GATK (view source)

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-However, GenomeAnalysisTK.jar must be in PATH. On our systems, the environmental variables <code>$EBROOTPICARD</code> for Picard (included in GATK >= 4) and <code>$EBROOTGATK</code> for GATK contain the path to the jar file, so the appropriate way to call GATK <= 3 is:
+However, GenomeAnalysisTK.jar must be in PATH. On our systems, the environmental variables <code>$EBROOTPICARD</code> for Picard (included in GATK >= 4) and <code>$EBROOTGATK</code> for GATK contain the path to the jar file, so the appropriate way to call GATK <= 3 is
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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 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 <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 provides <b>some</b> [https://gatk.broadinstitute.org/hc/en-us/articles/360035890591-Spark SPARK commands]:
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