Article
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets.
Nature communications - 16 Sept 2020
Berger Emily, Yorukoglu Deniz, Zhang Lillian, Nyquist Sarah K, Shalek Alex K, Kellis Manolis, Numanagić Ibrahim, Berger Bonnie
Abstract excerpt
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...
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