Genome editing based on CRISPR systems has been widely used in the vast areas of biomedical and agricultural applications. 

However, identifying the potential off-target sites remains challenging, particularly in individuals with diverse genetic variations. 

Several in silico tools have been developed to predict potential off-target sites, but they have limitations on their performance and scalability. 

In this paper, we present "Variant-aware Cas-OFFinder," a novel pipeline based on Cas-OFFinder for identifying potential off-target sites by accounting for individual genetic variants.

We benchmarked the pipeline's improved scalability and performance with the human genome and pepper cultivars, having unique potential off-target sites on each allele at the haplotype level. 

The web tool is open to all users without a login requirement and is freely available online at https://rgetoolkit.com/var-cas-offinder.

Nucleic Acids Res. 2025 May 8:gkaf389.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf389/8126898?login=true