Variant-aware Cas-OFFinder

A webtool for searching potential off-target sites accounting for genomic variants

Variant-aware Cas-OFFinder is a web-based tool for identifying potential CRISPR off-target sites across different genomes. It accounts for both reference genomes and individual genetic variants to improve accuracy in diverse populations. This addresses limitations caused by incomplete representation of genetic variation in reference genomes. Variant-aware Cas-OFFinder is freely available under GNU AGPL.

Citation info: Mekonnen, A. M., Seong, K., Kim, H., & Park, J. (2025). Variant-aware Cas-OFFinder: web-based in silico variant-aware potential off-target site identification for genome editing applications. Nucleic Acids Research, gkaf389.

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Upload VCF file
The VCF file should be phased and contain only one sample. Chromosome names in the vcf file and in the indexed refernce genome should be identical.

Download an example VCF file

Select pam Type

Select Target Genome

Query Sequences without pam from 5' to 3'

Maximum number of mismatches between gRNA and the target