title: scphaser: haplotype inference using single-cell RNA-seq data.
abstract: 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.
  
  
  
  scphaser is implemented as an R package. Tutorial and code are available at https://github.com/edsgard/scphaser
  
  
  
  rickard.sandberg@ki.se
  
  
  
  Supplementary data are available at Bioinformatics online.
authors: Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
authors: Daniel
authors: D
authors: Edsgärd
authors: Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
authors: Björn
authors: B
authors: Reinius
authors: Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden Ludwig Institute for Cancer Research, Box 240, 171 77 Stockholm, Sweden.
authors: Rickard
authors: R
authors: Sandberg
mesh_terms: D000483:Alleles; D000818:Animals; D014644:Genetic Variation; D006239:Haplotypes; D006801:Humans; D051379:Mice; D012313:RNA; D059010:Single-Cell Analysis
chemical_list: D012313:RNA