Table 2 Performance effect of Java, parallel garbage collection and temporary I/O directory tuning parameters.
From: Accelerating next generation sequencing data analysis with system level optimizations
GATK version | Java version | Parallel GC option | Java temporary I/O directory | HaplotypeCaller execution time (in Hours) |
|---|---|---|---|---|
GATK3.3_src | Java 1.7 | N/A | /tmp | 5.26 |
Java 1.7 | Parallel GC = 32 | /tmp | 3.81 | |
Java 1.7 | Parallel GC = 32 | /gpfs | 5.03 | |
GATK3.3_src | Java 1.8 | Parallel GC = 32 | /gpfs | 4.78 |
Java 1.8 | Parallel GC = 32 | — | 2.51 | |
Java 1.8 | CMS GC | — | 2.52 | |
GATK 3.7_jar | Java 1.8 | Parallel GC = 32 | — | 1.17 |
GATK 3.7_src | Java 1.8 | Parallel GC = 32 | — | 1.14 |
