DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework

Table 1

Comparison of variant calling results of DeepVariant and DeepVariant-on-Spark with different combinations of CPUs/GPUs.

Variant calling pipeline	Variant type	CPU^a	GPU^b	F1^c	Recall	Precision	True positive	False negative	False positive	Genotype mismatch	Total number of SNV calls
DeepVariant	SNP	16	0	0.99940	0.99937	0.99943	3040855	1928	1744	363	3886287
		32	0	0.99940	0.99937	0.99943	3040856	1927	1744	363	3886337
		64	0	0.99940	0.99937	0.99943	3040856	1927	1744	363	3886366
		96	0	0.99940	0.99937	0.99943	3040855	1928	1744	363	3886339
		16	1	0.99940	0.99937	0.99943	3040855	1928	1744	363	3886287
		16	4	0.99940	0.99937	0.99943	3040855	1928	1744	363	3886287
		32	2	0.99940	0.99937	0.99943	3040856	1927	1744	363	3886337
		64	4	0.99940	0.99937	0.99943	3040856	1927	1744	363	3886366
DeepVariant-on-Spark		32	0	0.99940	0.99937	0.99943	3040856	1927	1744	363	3886403
		64	0	0.99940	0.99937	0.99943	3040856	1927	1744	363	3886403
		128	0	0.99940	0.99937	0.99943	3040856	1927	1744	363	3886403
		32	2	0.99940	0.99937	0.99943	3040856	1927	1744	363	3886403
		64	4	0.99940	0.99937	0.99943	3040856	1927	1744	363	3886404
		128	8	0.99940	0.99937	0.99943	3040856	1927	1744	363	3886403
DeepVariant	Indel	16	0	0.96168	0.95711	0.96628	478265	21432	17373	11151	868527
		32	0	0.96168	0.95711	0.96628	478265	21432	17373	11151	868535
		64	0	0.96168	0.95711	0.96628	478265	21432	17373	11151	868520
		96	0	0.96168	0.95711	0.96628	478265	21432	17373	11151	868535
		16	1	0.96168	0.95711	0.96628	478265	21432	17373	11151	868527
		16	4	0.96168	0.95711	0.96628	478265	21432	17373	11151	868528
		32	2	0.96168	0.95711	0.96628	478265	21432	17373	11151	868535
		64	4	0.96168	0.95711	0.96628	478265	21432	17373	11151	868520
DeepVariant-on-Spark		32	0	0.96168	0.95711	0.96628	478265	21432	17373	11151	868541
		64	0	0.96168	0.95711	0.96628	478265	21432	17373	11151	868541
		128	0	0.96168	0.95711	0.96628	478265	21432	17373	11151	868541
		32	2	0.96168	0.95711	0.96628	478265	21432	17373	11151	868542
		64	4	0.96168	0.95711	0.96628	478265	21432	17373	11151	868542
		128	8	0.96168	0.95711	0.96628	478265	21432	17373	11151	868541

^aCPU means the number of CPU cores. ^bGPU means the number of NVIDIA Tesla P100 GPUs. ^cF1 means F1 score calculated by .