diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java
index c43106eec..90bb95b5b 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java
@@ -86,8 +86,6 @@ public class CustomAFPriorProvider extends AFPriorProvider {
 
     @Override
     protected double[] buildPriors(final int totalPloidy) {
-        if (totalPloidy != priors.length - 1)
-            throw new IllegalStateException("requesting an invalid prior total ploidy " + totalPloidy + " != " + (priors.length - 1));
         return priors;
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index 8ddfe3123..00f08851c 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -700,4 +700,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         spec.disableShadowBCF();
         executeTest("testHomRefHighMQ", spec);
     }
+
+    @Test
+    public void testInputPrior() {
+        final WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(" -V " + privateTestDir + "gvcfExample1.vcf -V " + privateTestDir + "gvcfExample2.vcf " +
+                        "-L 1:69485-69791 -inputPrior 0.2 -inputPrior 0.2 -inputPrior 0.2 -inputPrior 0.2", b37KGReference),
+                Collections.singletonList("860d133262160bbc75ce5849e5fa491f"));
+        spec.disableShadowBCF();
+        executeTest("testInputPrior", spec);
+    }
 }
\ No newline at end of file