diff --git a/pyproject.toml b/pyproject.toml
index 2e9f4329..230974d5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,7 @@ dependencies = [
   "matplotlib==3.8.1",
   "memory-efficient-attention-pytorch==0.1.6",
   "pandas==2.1.3",
-  "pybedtools==0.9.1",
+  "pybedtools==0.12.0",
   "seaborn==0.13.0",
   "sourmash==4.8.4",
   "torch==2.3.1",