HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing.

ABSTRACT:

Motivation

In diploid organisms, phasing is the problem of assigning the alleles at heterozygous variants to one of two haplotypes. Reads from PacBio HiFi sequencing provide long, accurate observations that can be used as the basis for both calling and phasing variants. HiFi reads also excel at calling larger classes of variation, such as structural or tandem repeat variants. However, current phasing tools typically only phase small variants, leaving larger variants unphased.

Results

We developed HiPhase, a tool that jointly phases SNVs, indels, structural, and tandem repeat variants. The main benefits of HiPhase are (i) dual mode allele assignment for detecting large variants, (ii) a novel application of the A*-algorithm to phasing, and (iii) logic allowing phase blocks to

SUBMITTER: Holt JM 

PROVIDER: S-EPMC10868326 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature