M2 doesn't use very short stubs of clipped reads for genotyping

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java

@@ -60,6 +60,11 @@ public final class Mutect2Engine implements AssemblyRegionEvaluator {
     public static final int MAX_NORMAL_QUAL_SUM = 100;
     public static final int MIN_PALINDROME_SIZE = 5;
 
+    // after trimming to fit the assembly window, throw away read stubs shorter than this length
+    // if we don't, the several bases left of reads that end just within the assembly window can
+    // get realigned incorrectly.  See https://github.com/broadinstitute/gatk/issues/5060
+    public static final int MINIMUM_READ_LENGTH_AFTER_TRIMMING = 10;
+
     private M2ArgumentCollection MTAC;
     private SAMFileHeader header;
 
@@ -193,6 +198,9 @@ public List<VariantContext> callRegion(final AssemblyRegion originalAssemblyRegi
         }
 
         final AssemblyRegion regionForGenotyping = assemblyResult.getRegionForGenotyping();
+        final List<GATKRead> readStubs = regionForGenotyping.getReads().stream()
+                .filter(r -> r.getLength() < MINIMUM_READ_LENGTH_AFTER_TRIMMING).collect(Collectors.toList());
+        regionForGenotyping.removeAll(readStubs);
 
         final Map<String,List<GATKRead>> reads = splitReadsBySample( regionForGenotyping.getReads() );
 

src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java

@@ -46,6 +46,10 @@ public class Mutect2IntegrationTest extends CommandLineProgramTest {
     private static final File NO_CONTAMINATION_TABLE = new File(toolsTestDir, "mutect/no-contamination.table");
     private static final File FIVE_PCT_CONTAMINATION_TABLE = new File(toolsTestDir, "mutect/five-pct-contamination.table");
     private static final File TEN_PCT_CONTAMINATION_TABLE = new File(toolsTestDir, "mutect/ten-pct-contamination.table");
+
+    private static final File NA12878_MITO_BAM = new File(toolsTestDir, "mutect/mito/NA12878.bam");
+    private static final File MITO_REF = new File(toolsTestDir, "mutect/mito/Homo_sapiens_assembly38.mt_only.fasta");
+
     /**
      * Several DREAM challenge bams with synthetic truth data.  In order to keep file sizes manageable, bams are restricted
      * to chromosome 20, leaving ~100-200 variants, and then further restricted to 400-bp intervals centered around
@@ -466,6 +470,35 @@ public void testMinBaseQualityScore() throws Exception {
         }
     }
 
+    // basic test on a small chunk of NA12878 mitochondria.  This is not a validation, but rather a sanity check
+    // that M2 makes obvious calls, doesn't trip up on the beginning of the circular chromosome, and can handle high depth
+    @Test
+    public void testMitochondria() throws Exception {
+        Utils.resetRandomGenerator();
+        final File unfilteredVcf = createTempFile("unfiltered", ".vcf");
+
+        final List<String> args = Arrays.asList("-I", NA12878_MITO_BAM.getAbsolutePath(),
+                "-" + M2ArgumentCollection.TUMOR_SAMPLE_SHORT_NAME, "NA12878",
+                "-R", MITO_REF.getAbsolutePath(),
+                "-L", "chrM:1-1000",
+                "-min-pruning", "5",
+                "-O", unfilteredVcf.getAbsolutePath());
+        runCommandLine(args);
+
+
+        final List<VariantContext> variants = VariantContextTestUtils.streamVcf(unfilteredVcf).collect(Collectors.toList());
+        final Set<String> variantKeys = variants.stream().map(vc -> keyForVariant(vc)).collect(Collectors.toSet());
+
+        final List<String> expectedKeys = Arrays.asList(
+                "chrM:152-152 [T*, C]",
+                "chrM:263-263 [A*, G]",
+                "chrM:301-301 [A*, AC]",
+                "chrM:302-302 [A*, AC, C, ACC]",
+                "chrM:310-310 [T*, TC]",
+                "chrM:750-750 [A*, G]");
+        Assert.assertTrue(expectedKeys.stream().allMatch(variantKeys::contains));
+    }
+
 
 
     @DataProvider(name="bamoutVariations")

src/test/resources/org/broadinstitute/hellbender/tools/mutect/mito/Homo_sapiens_assembly38.mt_only.dict

@@ -0,0 +1,2 @@
+@HD	VN:1.5
+@SQ	SN:chrM	LN:16569	M5:c68f52674c9fb33aef52dcf399755519	UR:file:/humgen/gsa-hpprojects/dev/mshand/SpecOps/Mitochondria/MitochondriaOnlyFastas/Homo_sapiens_assembly38.mt_only.fasta