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. 2020 Sep 1;2020:7231205. doi: 10.1155/2020/7231205

Table 1.

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

Variant calling pipeline Variant type CPUa GPUb F1c 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 2∗(recall∗precision)/(recall + precision).