Near perfect identification of half sibling versus niece/nephew avuncular pairs without pedigree information or genotyped relatives

We present a novel computational framework that achieves near-complete separation of HS and N/A pairs using only genotype data. Our approach utilizes across-chromosome phasing to derive haplotype-level sharing features that summarize how IBD is distributed across parental homologues. By modeling these features with a Gaussian mixture model (GMM), we demonstrate near-perfect classification accuracy (> 98%) in biobank-scale data. Furthermore, we show that these high-confidence relationship labels can serve as long-range phasing anchors, providing structural constraints that improve the accuracy of across-chromosome homologue assignment. This method provides a robust, scalable solution for pedigree reconstruction and the control of cryptic relatedness in large-scale genomic studies.