Differences

This shows you the differences between two versions of the page.

--- gatk-software [2023/05/11 09:59] – aorth
+++ gatk-software [2026/07/14 06:11] (current) – external edit 127.0.0.1
@@ 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 ======