BCFtools/liftover is a tool for converting genetic variants across genome assemblies. It improves support for indels and multi-allelic variants, and supports updating variant annotation fields when reference alleles change. It has a lower rate of variant drops and is faster than other tools. It is particularly suited for converting variant callsets from large cohorts to novel telomere-to-telomere assemblies and for summary statistics from genome-wide association studies tied to legacy genome assemblies. The tool is written in C and freely available under the MIT license. It is effective for converting genomic coordinates between assemblies, especially for indels and multi-allelic variants. It handles complex variants and supports updating variant annotations. It is faster and more accurate than other tools, and is suitable for converting variants between different genome assemblies, including between human and chimpanzee genomes. It also supports updating variant annotations and is efficient in terms of speed and memory usage. BCFtools/liftover is an accurate and comprehensive tool for converting genomic coordinates of VCF records from large cohorts, outperforming other tools in handling indels and multi-allelic variants. It is particularly useful for converting variants between different genome assemblies, including between human and chimpanzee genomes. It is also efficient in terms of speed and memory usage.BCFtools/liftover is a tool for converting genetic variants across genome assemblies. It improves support for indels and multi-allelic variants, and supports updating variant annotation fields when reference alleles change. It has a lower rate of variant drops and is faster than other tools. It is particularly suited for converting variant callsets from large cohorts to novel telomere-to-telomere assemblies and for summary statistics from genome-wide association studies tied to legacy genome assemblies. The tool is written in C and freely available under the MIT license. It is effective for converting genomic coordinates between assemblies, especially for indels and multi-allelic variants. It handles complex variants and supports updating variant annotations. It is faster and more accurate than other tools, and is suitable for converting variants between different genome assemblies, including between human and chimpanzee genomes. It also supports updating variant annotations and is efficient in terms of speed and memory usage. BCFtools/liftover is an accurate and comprehensive tool for converting genomic coordinates of VCF records from large cohorts, outperforming other tools in handling indels and multi-allelic variants. It is particularly useful for converting variants between different genome assemblies, including between human and chimpanzee genomes. It is also efficient in terms of speed and memory usage.