scphaser: haplotype inference using single-cell RNA-seq data

Summary: Determination of haplotypes is important for modelling the phenotypic consequences of genetic variation in diploid organisms, including cis-regulatory control and compound heterozygosity. We realized that single-cell RNA-seq (scRNA-seq) data are well suited for phasing genetic variants, since both transcriptional bursts and technical bottlenecks cause pronounced allelic fluctuations in individual single cells. Here we present scphaser, an R package that phases alleles at heterozygous variants to reconstruct haplotypes within transcribed regions of the genome using scRNA-seq data. The devised method efficiently and accurately reconstructed the known haplotype for ≥93% of phasable genes in both human and mouse. It also enables phasing of rare and de novo variants and variants far apart within genes, which is hard to attain with population-based computational inference. Availability and Implementation: scphaser is implemented as an R package. Tutorial and code are available at https://github.com/edsgard/scphaser Contact: rickard.sandberg@ki.se Supplementary information: Supplementary data are available at Bioinformatics online.