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/[e-mail] data are available at Bioinformatics online.

SUBMITTER: Edsgard D 

PROVIDER: S-EPMC5039928 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature