Recommendations for performance optimizations when using GATK3.8 and GATK4

BMC Bioinformatics

Table 3 Summary of optimized parameter values

Tool name	GATK3.8		GATK4
	PGC	Tool threads	PGC	Async	AVX threads
MarkDuplicates	2 threads	1	2 threads	N/A	N/A
BaseRecalibrator	20 threads	-nct 40	20 threads	Yes for Samtools, No for Tribble	N/A
ApplyBQSR	off	-nct 3	off		N/A
HaplotypeCaller	off	-nt 1 -nct 39	off		8

ISSN: 1471-2105