Fig. 3: Assessment of ClinVar variants predicted to be missed using Illumina and HiFi calls from DeepVariant.
From: StratoMod: predicting sequencing and variant calling errors with interpretable machine learning
a, b Heatmap of variants with a 10% or higher likelihood of being predicted as missed unshared between Illumina/Hifi (a) or shared (b) showing contributions of each feature within the model. Note that all interaction terms were added to their univariate main effect features to simplify visualization, and also note that negative scores contributed positively to a missed variant. c Predicted probabilities between Illumina and Hifi models. Red dotted red line is equal probability for Illumina and Hifi. Blue dotted lines are 90% probability cutoffs for either platform d ClinVar variant that is correctly predicted to be missed in Illumina-DeepVariant and as a TP in HiFi-DeepVariant due to being in a difficult-to-map region in a segmental duplication in PI4KA.
