Skip to main content

Table 1 Indel results for HG003 Whole Genome Sequencing (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 0.977132 0.962505 30,699 0.980459 0.971863 24,345 0.986638 0.973921 20,052
30x 0.987019 0.981851 15,934 0.991070 0.987324 11,067 0.994046 0.987738 9284
40x 0.990826 0.988121 10,801 0.994484 0.991528 7164 0.996235 0.990973 6516
50x 0.992820 0.991235 8191 0.996153 0.993191 5451 0.997263 0.992274 5325
  1. Values in bold indicate the best operating point for each tool for the corresponding metric