Fig. 6.

Imputation accuracy of 1KGP reference panel. (A) Variant sites covered by DV-GLN-OPT and GATK panel. The DV-GLN-OPT reference panel generated from 1KGP samples covers 43 181 562 variant sites, while the GATK panel from the same samples covers 41 247 330 sites. The intersection of the two panel regions (marked in light blue) covers 40 972 007 sites, which is 94.88% of the DV-GLN-OPT panel and 99.33% of the GATK panel. (B) Imputed genotype accuracy for indels. The accuracy of the imputed variants are measured by computing concordance with the GIAB benchmark calls using hap.py. Blue colored markers are from DV-GLN-OPT panel while the red markers are from GATK panel. The shaped markers show precision and recall computed across the GIAB evaluation region for two samples. (C) Imputed genotype accuracy for SNPs. Shapes and colors as in (B)