Figure 4.

Ideogram comparison of autosomal SNV recall at 8× for PacBio HiFi. (A) PacBio HiFi (8×) read-based recall of HG002 SNVs against GIAB truth sets. A bar over a chromosome depicts a 1 Mbp window where there was <90% SNV recall for Clair3 (green) and DeepVariant (orange) with all regions where SNVs were called in black. Highlighted regions represent limitations in methodology at low coverage. (B) PacBio HiFi (8×) assembly-based recall of HG002 GIAB SNV truth set using PAV. There are more 1 Mbp windows with <90% recall irrespective of assembly algorithm including hifiasm-trio (yellow), PGAS (blue), or hifiasm (gray).