HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing.
Bioinformatics
; 40(2)2024 02 01.
Article
em En
| MEDLINE
| ID: mdl-38269623
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 span breaks caused by alignment issues around reference gaps and homozygous deletions. In our assessment, HiPhase produced an average phase block NG50 of 480 kb with 929 switchflip errors and fully phased 93.8% of genes, improving over the current state of the art. Additionally, HiPhase jointly phases SNVs, indels, structural, and tandem repeat variants and includes innate multi-threading, statistics gathering, and concurrent phased alignment output generation. AVAILABILITY AND IMPLEMENTATION HiPhase is available as source code and a pre-compiled Linux binary with a user guide at https//github.com/PacificBiosciences/HiPhase.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Genoma Humano
/
Sequenciamento de Nucleotídeos em Larga Escala
Limite:
Humans
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article