Overview of variant classification using PeCanPIE. (A) Overview of processing steps from VCF through ACMG-based classification. Variant counts at each processing step for whole-exome sequencing data generated from a germline sample of a patient with acute lymphoblastic leukemia (ALL), SJNORM015857_G1 (Methods) (B) and whole-genome sequencing data generated from Genome in a Bottle normal sample NA12878_HG001 (Methods) (C).