BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies.

ABSTRACT:

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 coordinate

SUBMITTER: Genovese G 

PROVIDER: S-EPMC10832354 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature