Allele-specific maps

RPE-1 phased SNPs were obtained from a recent study of RPE-1 cell haplotyping from long-range sequencing (Tourdot et al. 2021). We examined Hi-C read-pairs with MAPQ ≥ 10 where at least one read was overlapping one or more informative SNPs and annotated each informative position to the A or B allele according to the phased information. Reads with varying allele assignments were discarded. Intrachromosomal read-pairs having only one of the reads phased were inferred to the same allele as the phased read. For interchromosomal events, we required both reads to span at least one informative SNP each. Applying these filters yielded allele-specific Hi-C maps with ∼12% of the full set of valid Hi-C interactions.