diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 401228c8..f1b659e4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -84,10 +84,10 @@ jobs:
           fetch-depth: 0  # Baseline comparison needs older commits
       - name: Install Linux dependencies
         if: runner.os == 'Linux'
-        run: sudo apt-get install samtools python3-pysam picard-tools
+        run: sudo apt-get install samtools python3-pysam picard-tools libisal-dev
       - name: Install macOS dependencies
         if: runner.os == 'macOS'
-        run: brew install samtools pysam picard-tools
+        run: brew install samtools pysam picard-tools isa-l
       - name: Cache test dataset
         uses: actions/cache@v4
         with: