From: Recommendations for performance optimizations when using GATK3.8 and GATK4
GATK version | Splitting | Samples | Nodes | Walltime, hrs | c5.9xlarge | c5.18xlarge |
---|---|---|---|---|---|---|
GATK 4.0.1.2 | no splitting | 1 | 1 | 20.7 | $31.7 | $63.3 |
GATK 3.8 | no splitting | 1 | 1 | 15.3 | $23.4 | $46.8 |
GATK 3.8 | 12 chunks | 1 | 4 | 3.4 | $20.8 | $41.6 |
GATK 3.8 | 6 chunks | 1 | 2 | 4.7 | $14.4 | $28.8 |
GATK 3.8 | 16 chunks | 1 | 1 | 5.0 | $7.7 | $15.3 |
GATK 4.0.1.2 | 16 chunks | 1 | 1 | 3.6 | $5.5 | $11.0 |
GATK 4.0.1.2 | no splitting | 40 | 1 | 34.1 | $1.3 | $2.6 |