diff --git a/partition-before-pggb b/partition-before-pggb
index 30dd1a7..36e4b86 100755
--- a/partition-before-pggb
+++ b/partition-before-pggb
@@ -276,11 +276,15 @@ check_tool_availability "seqwish" "seqwish"
 check_tool_availability "smoothxg" "smoothxg"
 check_tool_availability "odgi" "odgi"
 check_tool_availability "gfaffix" "gfaffix"
+if [ "$vcf_spec" != "false" ]; then
 check_tool_availability "vg" "vg"
 check_tool_availability "vcfbub" "vcfbub"
 check_tool_availability "vcfwave" "vcfwave"
 check_tool_availability "bcftools" "bcftools"
+fi
+if [[ $multiqc == true ]]; then
 check_tool_availability "MultiQC" "multiqc"
+fi
 
 # If there are missing tools, report them and exit
 if [ ${#missing_tools[@]} -ne 0 ]; then
diff --git a/pggb b/pggb
index 9765353..ad3b772 100755
--- a/pggb
+++ b/pggb
@@ -276,11 +276,15 @@ check_tool_availability "seqwish" "seqwish"
 check_tool_availability "smoothxg" "smoothxg"
 check_tool_availability "odgi" "odgi"
 check_tool_availability "gfaffix" "gfaffix"
+if [ "$vcf_spec" != "false" ]; then
 check_tool_availability "vg" "vg"
 check_tool_availability "vcfbub" "vcfbub"
 check_tool_availability "vcfwave" "vcfwave"
 check_tool_availability "bcftools" "bcftools"
+fi
+if [[ $multiqc == true ]]; then
 check_tool_availability "MultiQC" "multiqc"
+fi
 
 # If there are missing tools, report them and exit
 if [ ${#missing_tools[@]} -ne 0 ]; then