Fig 2 Variant Calling Performance HG003

Figure 2. Variant Calling Performance, HG003. Total errors – the sum of SNV and indel false positives (FP) and false negatives (FN) – in a DeepVariant callset from 35× PacBio HiFi read coverage (Sequel II System, Chemistry 2.0); a DeepVariant callset from 35× Illumina NovaSeq; a GATK 4 callset from 35× Illumina NovaSeq; and a PEPPER-DeepVariant callset from 60× ONT PromethION R9.4.1. Performance is measured with hap.py against the Genome in a Bottle small variant benchmark v4.2 used in the precisionFDA Truth Challenge V2. The PacBio HiFi DeepVariant callset had the fewest overall errors of any single-technology callset in the challenge.