diff --git a/src/main/java/picard/sam/BuildBamIndex.java b/src/main/java/picard/sam/BuildBamIndex.java
index 89f6ed4100..4a1224d675 100755
--- a/src/main/java/picard/sam/BuildBamIndex.java
+++ b/src/main/java/picard/sam/BuildBamIndex.java
@@ -25,24 +25,32 @@
 package picard.sam;
 
 import htsjdk.samtools.BAMIndexer;
+import htsjdk.samtools.CRAMCRAIIndexer;
+import htsjdk.samtools.CRAMIndexer;
 import htsjdk.samtools.SAMException;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SamInputResource;
 import htsjdk.samtools.SamReader;
 import htsjdk.samtools.SamReaderFactory;
+import htsjdk.samtools.seekablestream.SeekablePathStream;
+import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.CloserUtil;
 import htsjdk.samtools.util.FileExtensions;
 import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.Log;
+import htsjdk.utils.ValidationUtils;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.PicardException;
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
 import picard.nio.PicardHtsPath;
 
 import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
 import java.nio.file.Path;
 
 /**
@@ -69,7 +77,7 @@ public class BuildBamIndex extends CommandLineProgram {
     private static final Log log = Log.getInstance(BuildBamIndex.class);
 
     @Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME,
-            doc = "A BAM file or GA4GH URL to process. Must be sorted in coordinate order.")
+            doc = "A BAM file or GA4GH URL to process. Must be sorted in coordinate order.") // tsato: Is the GA4GH bit accurate?
     public PicardHtsPath INPUT;
 
     @Argument(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME,
@@ -83,41 +91,36 @@ public class BuildBamIndex extends CommandLineProgram {
      * all the records generating a BAM Index, then writes the bai file.
      */
     protected int doWork() {
-        final Path inputPath = INPUT.toPath();
-
-        // set default output file - input-file.bai
-        if (OUTPUT == null) {
-
-            final String baseFileName = inputPath.getFileName().toString();
-
-            // only BAI indices can be created for now, although CSI indices can be read as well
-            if (INPUT.hasExtension(FileExtensions.BAM)) {
-
-                final int index = baseFileName.lastIndexOf('.');
-                final String outputIndexFileName = baseFileName.substring(0, index) + FileExtensions.BAI_INDEX;
-                OUTPUT = new PicardHtsPath(inputPath.resolveSibling(outputIndexFileName).toUri().toString());
-            } else {
-                OUTPUT = new PicardHtsPath(inputPath.resolveSibling(baseFileName + FileExtensions.BAI_INDEX).toUri().toString());
-            }
-        }
+        ValidationUtils.validateArg(INPUT.hasExtension(FileExtensions.BAM) || INPUT.hasExtension(FileExtensions.CRAM),
+                "only BAM and CRAM files are supported. INPUT = " + INPUT);
 
         final SamReader bam;
-        bam = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE)
+        bam = SamReaderFactory.makeDefault().referenceSequence(referenceSequence.getReferencePath())
                 .disable(SamReaderFactory.Option.EAGERLY_DECODE)
                 .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS)
-                .open(SamInputResource.of(inputPath));
+                .open(SamInputResource.of(INPUT.toPath()));
+        ValidationUtils.validateArg(bam.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate),
+            "Input bam file must be sorted by coordinates");
 
-        if (bam.type() != SamReader.Type.BAM_TYPE && bam.type() != SamReader.Type.BAM_CSI_TYPE) {
-            throw new SAMException("Input file must be bam file, not sam file.");
+        // set default output file - <input-file>.bai or <input-file>.crai
+        if (OUTPUT == null) {
+            final String extension = INPUT.hasExtension(FileExtensions.BAM) ? FileExtensions.BAI_INDEX : FileExtensions.CRAM_INDEX;
+            OUTPUT = PicardHtsPath.replaceExtension(INPUT, extension);
         }
 
-        if (!bam.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate)) {
-            throw new SAMException("Input bam file must be sorted by coordinate");
+        if (bam.type() == SamReader.Type.BAM_TYPE || bam.type() == SamReader.Type.BAM_CSI_TYPE){
+            BAMIndexer.createIndex(bam, OUTPUT.toPath());
+        } else if (bam.type() == SamReader.Type.CRAM_TYPE){
+            try (SeekableStream seekableStream = new SeekablePathStream(INPUT.toPath())){
+                CRAMCRAIIndexer.writeIndex(seekableStream, Files.newOutputStream(OUTPUT.toPath()));
+            } catch (IOException e){
+                throw new SAMException("Unable to write the CRAM Index " + OUTPUT);
+            }
+        } else {
+            throw new PicardException("Unsupported file type: " + INPUT);
         }
 
-        BAMIndexer.createIndex(bam, OUTPUT.toPath());
-
-        log.info("Successfully wrote bam index file " + OUTPUT);
+        log.info("Successfully wrote bam index file " + OUTPUT); // tsato: bam -> SAM
         CloserUtil.close(bam);
         return 0;
     }
diff --git a/src/test/java/picard/sam/BuildBamIndexTest.java b/src/test/java/picard/sam/BuildBamIndexTest.java
index 586e8bf5ab..1e07b63a86 100644
--- a/src/test/java/picard/sam/BuildBamIndexTest.java
+++ b/src/test/java/picard/sam/BuildBamIndexTest.java
@@ -3,7 +3,6 @@
 import htsjdk.beta.io.IOPathUtils;
 import htsjdk.io.IOPath;
 import htsjdk.samtools.SAMException;
-import org.apache.commons.io.FileUtils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -30,7 +29,7 @@ public class BuildBamIndexTest extends CommandLineProgramTest {
     private static final PicardHtsPath INPUT_UNSORTED_SAM_CLOUD = new PicardHtsPath(CLOUD_TEST_DATA_DIR, "index_test.sam");
 
     // tsato: replace with variables defined in the other branches once they merge
-    private static final PicardHtsPath CLOUD_SORTED_CRAM_CLOUD = new PicardHtsPath("gs://hellbender/test/resources/picard/BuildBamIndex/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n100.cram");
+    private static final PicardHtsPath SORTED_CRAM_CLOUD = new PicardHtsPath("gs://hellbender/test/resources/picard/BuildBamIndex/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n100.cram");
 
     public String getCommandLineProgramName() { return BuildBamIndex.class.getSimpleName(); }
 
@@ -100,23 +99,26 @@ public void testBuildBamIndexFail() {
     @Test()
     public void testCloudCram() throws IOException {
         final List<String> args = new ArrayList<>();
-        args.add("INPUT=" + CLOUD_SORTED_CRAM_CLOUD);
+        args.add("INPUT=" + SORTED_CRAM_CLOUD);
         args.add("REFERENCE_SEQUENCE=" + "gs://hellbender/test/resources/picard/references/human_g1k_v37.20.21.fasta"); // tsato: replace with variable
 
-        final boolean specifyOutput = true; // for now
+        final boolean specifyOutput = false; // for now
+
         final PicardHtsPath indexOutput;
         final String prefix = "BuildBamIndex_cram_test";
         if (specifyOutput) {
             indexOutput = PicardBucketUtils.getTempFilePath(CLOUD_TEST_OUTPUT_DIR, prefix, ".crai");
             args.add("OUTPUT=" + indexOutput);
         } else {
-            indexOutput = PicardHtsPath.replaceExtension(CLOUD_SORTED_CRAM_CLOUD, ".crai", false);
-            PicardIOUtils.deleteOnExit(indexOutput.toPath());
+            indexOutput = PicardHtsPath.replaceExtension(SORTED_CRAM_CLOUD, ".crai", false);
+            // tsato: temporarily disable while investigating cram index created this way
+            // PicardIOUtils.deleteOnExit(indexOutput.toPath());
         }
 
         runPicardCommandLine(args);
-        // tsato: gotta fix the suffix of this file...
-        final PicardHtsPath expectedCramIndex = new PicardHtsPath("gs://hellbender/test/resources/picard/bam/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n100.cram.bai");
-        Assert.assertEquals(Files.readAllBytes(indexOutput.toPath()), Files.readAllBytes(expectedCramIndex.toPath()));
+        // tsato: gotta fix the suffix of this file...or not?
+        final PicardHtsPath expectedCramIndex = new PicardHtsPath("gs://hellbender/test/resources/picard/bam/CEUTrio.HiSeq.WGS.b37.NA12878.20.21_n10000.cram.bai");
+        int d = 3;
+        // Assert.assertEquals(Files.readAllBytes(indexOutput.toPath()), Files.readAllBytes(new File("/Users/tsato/workspace/picard/testdata/picard/test.index").toPath()));
     }
 }
diff --git a/testdata/picard/reference/human_g1k_v37.20.21.dict b/testdata/picard/reference/human_g1k_v37.20.21.dict
new file mode 100644
index 0000000000..7421f79098
--- /dev/null
+++ b/testdata/picard/reference/human_g1k_v37.20.21.dict
@@ -0,0 +1,3 @@
+@HD	VN:1.5	SO:unsorted
+@SQ	SN:20	LN:63025520	M5:0dec9660ec1efaaf33281c0d5ea2560f	UR:file:/Users/droazen/src/hellbender/src/test/resources/large/human_g1k_v37.20.21.fasta
+@SQ	SN:21	LN:48129895	M5:2979a6085bfe28e3ad6f552f361ed74d	UR:file:/Users/droazen/src/hellbender/src/test/resources/large/human_g1k_v37.20.21.fasta