diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
index ee5c59fd8..34b5a606f 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -608,8 +608,15 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     // reference base padding size
     private static final int REFERENCE_PADDING = 500;
 
-    private final static int maxReadsInRegionPerSample = 1000; // TODO -- should be an argument
-    private final static int minReadsPerAlignmentStart = 5; // TODO -- should be an argument
+    /**
+     * When downsampling, level the coverage of the reads in each sample to no more than maxReadsInRegionPerSample reads,
+     * not reducing coverage at any read start to less than minReadsPerAlignmentStart
+     */
+    @Argument(fullName = "maxReadsInRegionPerSample", shortName = "maxReadsInRegionPerSample", doc="Maximum reads in an active region", required = false)
+    protected int maxReadsInRegionPerSample = 1000;
+
+    @Argument(fullName = "minReadsPerAlignmentStart", shortName = "minReadsPerAlignStart", doc="Minimum number of reads sharing the same alignment start for each genomic location in an active region", required = false)
+    protected int minReadsPerAlignmentStart = 5;
 
     private byte MIN_TAIL_QUALITY;
     private static final byte MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION = 6;
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index a721f2d33..2853fce29 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -78,7 +78,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     final static String GGA_INTERVALS_FILE = privateTestDir + "haplotype-caller-reduced-test-interval.list";
 
     private void HCTest(String bam, String args, String md5) {
-        final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE -R %s -I %s -L %s", REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
+        final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE --maxReadsInRegionPerSample 1000 --minReadsPerAlignmentStart 5 -R %s -I %s -L %s", REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
         final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
         executeTest("testHaplotypeCaller: args=" + args, spec);
     }