SVUPP: Pre-phasing long reads improves structural variant genotyping.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41134129.
- Also identified by DOI 10.1093/bioinformatics/btaf587 and PMC identifier 12771361.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Here, we present an approach, called SVUPP, which improves genotyping of structural variant (SV) by incorporating read phasing information into genotype likelihoods. Through comprehensive benchmarking, we show that SVUPP achieved higher accuracy than cuteSV2, Sniffles2 and kanpig with both long and ultra long Oxford Nanopore Technologies (ONT) data as well as Pacific Biosciences (PacBio) HiFi data for genotyping SVs without close neighbor SVs. SVUPP can be applied together with SV callers such as cuteSV2 and take the per-read phasing information from reference panel based phasing method such as QUILT2 or from reference-free phasing method such as WhatsHap. SVUPP is written in Nextflow with modular design and is freely available here https://github.com/Zilong-Li/SVUPP.