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--- gatk-software [2023/05/11 09:59] – [Installation] aorth
+++ gatk-software [2026/01/09 09:46] (current) – aorth
@@ Line 19: / Line 19: @@
 $ gatk</code>
-**Note:** The HaplotypeCaller step can scale to multiple CPUs/threads. Please use the ''-nct'' option to set the number of threads launched by GATK. This number should be the same number of CPUs requested in your SLURM batch job.
+**Note:** As of GATK4 the HaplotypeCaller step can be replaced by [[https://gatk.broadinstitute.org/hc/en-us/articles/13832685403803-HaplotypeCallerSpark-BETA|HaplotypeCallerSpark]], which has better performance with multiple CPUs/threads. Please use the ''--native-pair-hmm-threads'' option to set the number of threads launched by GATK (default 4). This number should be the same number of CPUs requested in your SLURM batch job.
 ===== Installation ======
@@ Line 30: / Line 30: @@
 $ sudo cp -r gatk-4.4.0.0 /export/apps/gatk/4.4.0.0</code>
-//Note (2023-05-11)//: we are not currently satisfying Python or R dependencies here because I think most users are not using those features. See [[https://github.com/broadinstitute/gatk#requirements|the GATK requirements]] for more information.
+**Note (2023-05-11):** we are not currently satisfying Python or R dependencies here because I think most users are not using those features. See [[https://github.com/broadinstitute/gatk#requirements|the GATK requirements]] for more information.