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Table 3 Summary of optimized parameter values

From: Recommendations for performance optimizations when using GATK3.8 and GATK4

Tool nameGATK3.8GATK4
 PGCTool threadsPGCAsyncAVX threads
MarkDuplicates2 threads12 threadsN/AN/A
BaseRecalibrator20 threads-nct 4020 threadsYes for Samtools, No for TribbleN/A
ApplyBQSRoff-nct 3off N/A
HaplotypeCalleroff-nt 1 -nct 39off 8