Fig. 3

The necessity and possible benefit of variant filtering depends on the variant calling method. Shown are positive changes in precision (blue boxes) and negative changes in recall (yellow boxes) on SNPs and INDELs in WES and WGS data. Gray shading corresponds to cases where filtering is beneficial, i.e. gain in precision is greater than the loss of recall. Variant callers and filtering strategies: CL - Clair3, DV - DeepVariant, G1 - GATK HaplotypeCaller with 1D CNN filtering, G2 - GATK HaplotypeCaller with 2D CNN filtering, GH - GATK HaplotypeCaller with recommended hard filters. ST - Strelka2, FB - Freebayes, OS - Octopus with standard filtering, OF - Octopus with random forest filtering