Direct inference of haplotypes from sequencing data.

ABSTRACT:

Motivation

Haplotypes are crucial for various genetic analyses, but reconstructing haplotypes from sequencing data remains a significant challenge. Current methods for haplotype reconstruction typically rely on a procedure of two separated stages, variant calling and phasing, but phasing overlooks the errors in variant calling. Additionally, the complexity of haplotype reconstruction increases with the number of homologous chromosomes in the sample, a common scenario in polyploid species or cell mixture sequencing.

Results

To address the challenges above, we propose a unified probabilistic framework that directly utilizes sequencing reads to estimate haplotypes and sequencing error profiles. Rather than focusing solely on variant loci used by traditional phasing methods, our

SUBMITTER: Zhang Z 

PROVIDER: S-EPMC12448230 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature