diff --git a/.github/filters.yml b/.github/filters.yml
index 74156e9d..2141ce21 100644
--- a/.github/filters.yml
+++ b/.github/filters.yml
@@ -92,6 +92,14 @@ bwa_mem:
   - software/bwa/mem/**
   - tests/software/bwa/mem/**
 
+bwamem2_index:
+  - software/bwamem2/index/**
+  - tests/software/bwamem2/index/**
+
+bwamem2_mem:
+  - software/bwamem2/mem/**
+  - tests/software/bwamem2/mem/**
+
 cutadapt:
   - software/cutadapt/**
   - tests/software/cutadapt/**