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Table 2 SNV results for HG003 WGS, Illumina

From: HELLO: improved neural network architectures and methodologies for small variant calling

  GATK DeepVariant HELLO
Precision Recall Errors Precision Recall Errors Precision Recall Errors
20x 0.993089 0.987367 64,904 0.994664 0.990906 47,956 0.996837 0.990922 40,679
30x 0.992641 0.992285 50,157 0.996820 0.993576 31,928 0.998147 0.993197 28,776
40x 0.992119 0.993382 48,286 0.997644 0.994059 27,584 0.998533 0.993424 26,742
50x 0.991823 0.993881 47,633 0.998125 0.994017 26,125 0.998761 0.993395 26,082
  1. Values in bold indicate the best operating point for each tool for the corresponding metric