BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies
Average rating
Cast your vote
You can rate an item by clicking the amount of stars they wish to award to this item.
When enough users have cast their vote on this item, the average rating will also be shown.
Star rating
Your vote was cast
Thank you for your feedback
Thank you for your feedback
Author
Genovese, GiulioRockweiler, Nicole B
Gorman, Bryan R
Bigdeli, Tim B
Pato, Michelle T
Pato, Carlos N
Ichihara, Kiku
McCarroll, Steven A
Keyword
Computational MathematicsComputational Theory and Mathematics
Computer Science Applications
Molecular Biology
Biochemistry
Statistics and Probability
Journal title
BioinformaticsDate Published
2024-01-23Publication Volume
40Publication Issue
2
Metadata
Show full item recordAbstract
Motivation: Many genetics studies report results tied to genomic coordinates of a legacy genome assembly. However, as assemblies are updated and improved, researchers are faced with either realigning raw sequence data using the updated coordinate system or converting legacy datasets to the updated coordinate system to be able to combine results with newer datasets. Currently available tools to perform the conversion of genetic variants have numerous shortcomings, including poor support for indels and multi-allelic variants, that lead to a higher rate of variants being dropped or incorrectly converted. As a result, many researchers continue to work with and publish using legacy genomic coordinates. Results: Here we present BCFtools/liftover, a tool to convert genomic coordinates across genome assemblies for variants encoded in the variant call format with improved support for indels represented by different reference alleles across genome assemblies and full support for multi-allelic variants. It further supports variant annotation fields updates whenever the reference allele changes across genome assemblies. The tool has the lowest rate of variants being dropped with an order of magnitude less indels dropped or incorrectly converted and is an order of magnitude faster than other tools typically used for the same task. It is particularly suited for converting variant callsets from large cohorts to novel telomere-to-telomere assemblies as well as summary statistics from genome-wide association studies tied to legacy genome assemblies. Availability and implementation: The tool is written in C and freely available under the MIT open source license as a BCFtools plugin available at http://github.com/freeseek/score.Citation
Genovese G, Rockweiler NB, Gorman BR, Bigdeli TB, Pato MT, Pato CN, Ichihara K, McCarroll SA. BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies. Bioinformatics. 2024 Jan 2;40(2):btae038. doi: 10.1093/bioinformatics/btae038. PMID: 38261650; PMCID: PMC10832354.DOI
10.1093/bioinformatics/btae038ae974a485f413a2113503eed53cd6c53
10.1093/bioinformatics/btae038
Scopus Count
Collections
Except where otherwise noted, this item's license is described as https://creativecommons.org/licenses/by/4.0/
Related articles
- CrossMap: a versatile tool for coordinate conversion between genome assemblies.
- Authors: Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L
- Issue date: 2014 Apr 1
- Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data.
- Authors: Luu PL, Ong PT, Dinh TP, Clark SJ
- Issue date: 2020 Sep
- BCFtools/csq: haplotype-aware variant consequences.
- Authors: Danecek P, McCarthy SA
- Issue date: 2017 Jul 1
- segment_liftover : a Python tool to convert segments between genome assemblies.
- Authors: Gao B, Huang Q, Baudis M
- Issue date: 2018
- RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes.
- Authors: Liu W, Wu S, Lin Q, Gao S, Ding F, Zhang X, Aljohi HA, Yu J, Hu S
- Issue date: 2018 Oct