Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets.

ABSTRACT: Haplotype reconstruction of distant genetic variants remains an unsolved problem due to the short-read length of common sequencing data. Here, we introduce HapTree-X, a probabilistic framework that utilizes latent long-range information to reconstruct unspecified haplotypes in diploid and polyploid organisms. It introduces the observation that differential allele-specific expression can link genetic variants from the same physical chromosome, thus even enabling using reads that cover only individual variants. We demonstrate HapTree-X's feasibility on in-house sequenced Genome in a Bottle RNA-seq and various whole exome, genome, and 10X Genomics datasets. HapTree-X produces more complete phases (up to 25%), even in clinically important genes, and phases more variants than other methods whil

SUBMITTER: Berger E 

PROVIDER: S-EPMC7494856 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature