Fig. 4

Overview of the ASDPex algorithm. a ASDPex compares the set of all variants called against REF-HAP \(\mathcal {R}\) with the set of ASDPs associated with ALT-HAP \(\mathcal {A}\). In this example, \(\left | \mathcal {A}\right |\) (the number of ASDPs associated with ALT-HAP) is 6, and \(\left |\mathcal {R}\right |\) (the total number of variants called against REF-HAP) is 8. ASDPex defines the set of residual variants as the symmetric set difference between \(\mathcal {R}\) and \(\mathcal {A}\), i.e., \(\text {\texttt {RV}}=\mathcal {R} \triangle \mathcal {A}\). Therefore, |RV|=4, and because \(\left |\text {\texttt {RV}}\right | < \left |\mathcal {R}\right |\), our algorithm infers that ALT-HAP is present. b The pattern of variant calls obtained for ASDPs differs according to whether the sequenced proband is homozygous for one of the two alternate loci or is heterozygous. Our algorithm exploits this pattern across the entire length of the alternate locus to infer the most likely genotype. ASDP alignable scaffold-discrepant position