diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java
index 60048933599..f5f56a2483e 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java
@@ -433,10 +433,12 @@ static double[] getGermlineAltAlleleFrequencies(final List<Allele> allAlleles, f
             List<OptionalInt> germlineIndices = GATKVariantContextUtils.alleleIndices(allAlleles, germlineVC.getAlleles());
             final List<Double> germlineAltAFs = Mutect2Engine.getAttributeAsDoubleList(germlineVC, VCFConstants.ALLELE_FREQUENCY_KEY, afOfAllelesNotInGermlineResource);
 
-            for (int alleleIndex = 1; alleleIndex < allAlleles.size(); alleleIndex++) { // start at 1 to skip the reference, which doesn't have an AF annotation
-                final Allele allele = allAlleles.get(alleleIndex);
-                // note the -1 since germlineAltAFs do not include ref
-                germlineIndices.get(alleleIndex).ifPresent(germlineIndex -> alleleFrequencies.put(allele, germlineAltAFs.get(germlineIndex - 1)));
+            if (germlineAltAFs.size() == (germlineVC.getNAlleles() - 1)) {  // skip VCs with a bad AF field that got parsed as a wrong-length list
+                for (int alleleIndex = 1; alleleIndex < allAlleles.size(); alleleIndex++) { // start at 1 to skip the reference, which doesn't have an AF annotation
+                    final Allele allele = allAlleles.get(alleleIndex);
+                    // note the -1 since germlineAltAFs do not include ref
+                    germlineIndices.get(alleleIndex).ifPresent(germlineIndex -> alleleFrequencies.put(allele, germlineAltAFs.get(germlineIndex - 1)));
+                }
             }
         }