From ae1cd9b992d657c9d52db8e26cab3c374294abc3 Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Mon, 22 Jul 2019 16:11:48 -0400
Subject: [PATCH] Fixes for tests

---
 .../hellbender/engine/FeatureManager.java     |   2 +-
 .../hellbender/engine/VariantWalker.java      |  10 ----
 .../tools/evoquer/GnarlyGenotyperEngine.java  |   4 +-
 .../tools/genomicsdb/GenomicsDBOptions.java   |   2 +-
 .../tools/genomicsdb/GenomicsDBUtils.java     |   2 +-
 .../tools/walkers/GnarlyGenotyper.java        |  41 +++++++-------
 .../walkers/annotator/AnnotationUtils.java    |  13 ++---
 .../walkers/annotator/RMSMappingQuality.java  |  29 +++++-----
 .../allelespecific/AS_QualByDepth.java        |   6 +--
 .../allelespecific/AS_RMSMappingQuality.java  |   4 +-
 .../allelespecific/AS_RankSumTest.java        |   2 +-
 .../walkers/variantutils/ReblockGVCF.java     |   4 +-
 .../hellbender/utils/GenotypeUtils.java       |  30 +++++------
 .../utils/variant/GATKVCFConstants.java       |   2 +-
 .../utils/variant/GATKVCFHeaderLines.java     |   2 +-
 .../annotator/RMSMappingQualityUnitTest.java  |   4 +-
 ...S_Annotations.keepRawCombined.expected.vcf |  51 +++++++++---------
 ...hailOutput.chr20snippet.sites_only.vcf.idx | Bin 0 -> 154586 bytes
 18 files changed, 98 insertions(+), 110 deletions(-)
 create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/hailOutput.chr20snippet.sites_only.vcf.idx

diff --git a/src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java b/src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java
index 4b21f4ba893..7aaa1e8507c 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java
@@ -208,7 +208,7 @@ private void initializeFeatureSources( final int featureQueryLookahead, final Co
             if ( featureInput != null ) {
                 final Class<? extends Feature> featureType = getFeatureTypeForFeatureInputField(featureArgument.getKey());
                 addToFeatureSources(featureQueryLookahead, featureInput, featureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer,
-                        toolInstance instanceof GATKTool ? ((GATKTool) toolInstance).getGenomicsDBOptions() : null);
+                        toolInstance instanceof VariantWalker ? ((VariantWalker) toolInstance).getGenomicsDBOptions() : null);
             }
         }
     }
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/VariantWalker.java b/src/main/java/org/broadinstitute/hellbender/engine/VariantWalker.java
index 3d0e8b51cd6..3fb19ce414a 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/VariantWalker.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/VariantWalker.java
@@ -7,10 +7,8 @@
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.engine.filters.CountingReadFilter;
 import org.broadinstitute.hellbender.exceptions.GATKException;
-import org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 
-import java.nio.file.Path;
 import java.util.Spliterator;
 
 /**
@@ -146,12 +144,4 @@ protected final void onShutdown() {
         if ( drivingVariants != null )
             drivingVariants.close();
     }
-
-    /**
-     * Does this tool need sample genotypes to be called if reading from a GenomicsDB?
-     * @return if false, GTs remain no-calls, as in CombineGVCFs
-     */
-    protected boolean doGenotypeCalling() {
-        return false;
-    }
 }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/evoquer/GnarlyGenotyperEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/evoquer/GnarlyGenotyperEngine.java
index 6afd517644b..f304fd5d9bc 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/evoquer/GnarlyGenotyperEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/evoquer/GnarlyGenotyperEngine.java
@@ -68,7 +68,7 @@ public GnarlyGenotyperEngine(final boolean keepAllSites, final int maxAltAlleles
     }
 
     @SuppressWarnings({"unchecked", "rawtypes"})
-    public static VariantContext finalizeGenotype(final VariantContext variant, final VariantContextBuilder annotationDBBuilder) {
+    public VariantContext finalizeGenotype(final VariantContext variant, final VariantContextBuilder annotationDBBuilder) {
         //GenomicsDB or Evoquer merged all the annotations, but we still need to finalize MQ and QD annotations
         //return a VC with the finalized annotations and dbBuilder gets the raw annotations for the database
 
@@ -245,7 +245,7 @@ public static VariantContext finalizeGenotype(final VariantContext variant, fina
      * @param vc the input variant with NON_REF
      * @return a GenotypesContext
      */
-    private static GenotypesContext iterateOnGenotypes(final VariantContext vc, final List<Allele> targetAlleles,
+    private GenotypesContext iterateOnGenotypes(final VariantContext vc, final List<Allele> targetAlleles,
                                                 final Map<Allele,Integer> targetAlleleCounts, final int[] SBsum,
                                                 final boolean nonRefReturned, final boolean summarizePLs,
                                                 final int[] rawGenotypeCounts) {
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBOptions.java b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBOptions.java
index db37250cdbf..32516b9b2fb 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBOptions.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBOptions.java
@@ -23,7 +23,7 @@ public GenomicsDBOptions(final Path reference) {
     /**
      *
      * @param reference     Path to a reference. May be null. Needed only for reading from GenomicsDB.
-     * @param callGenotypes Indicated whether GenomicsDB should return called genotypes
+     * @param callGenotypes Indicates whether GenomicsDB should return called genotypes
      */
     public GenomicsDBOptions(final Path reference, final boolean callGenotypes, final int maxAlternateAlleles) {
         this.reference = reference;
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBUtils.java
index 3095874503a..cb1b41193e9 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBUtils.java
@@ -103,7 +103,7 @@ public static GenomicsDBExportConfiguration.ExportConfiguration createExportConf
         //Update combine operations for GnarlyGenotyper
         //Note that this MQ format is deprecated, but was used by the prototype version of ReblockGVCF
         vidMapPB = updateINFOFieldCombineOperation(vidMapPB, fieldNameToIndexInVidFieldsList,
-                GATKVCFConstants.MAPPING_QUALITY_DEPTH, "sum");
+                GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED, "sum");
         vidMapPB = updateINFOFieldCombineOperation(vidMapPB, fieldNameToIndexInVidFieldsList,
                 GATKVCFConstants.RAW_QUAL_APPROX_KEY, "sum");
         vidMapPB = updateINFOFieldCombineOperation(vidMapPB, fieldNameToIndexInVidFieldsList,
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper.java
index 39dbea2f2a9..88ae435e6c9 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper.java
@@ -70,8 +70,10 @@
  * </pre>
  *
  * <h3>Caveats</h3>
- * <p><ul><li>Only GenomicsDB instances can be used as input for this tool.</li>
- * <li>To generate all the annotations necessary for VQSR, input variants must include the QUALapprox, VarDP and MQ_DP
+ * <p><ul>
+ * <li>This tool does not subset to the best alternate alleles and can return highly, highly multialleic variants (>1000 alts for cohorts in the 10s of thousands). Only
+ * GenomicsDB instances should be used as input for this tool, because GenomicsDB will drop PLs for such sites to avoid excessive vcf size.</li>
+ * <li>To generate all the annotations necessary for VQSR, input variants must include the QUALapprox, VarDP and MQ_DP annotations
  * </ul></p>
  *
  * <h3>Special note on ploidy</h3>
@@ -82,6 +84,7 @@
         oneLineSummary = "Perform \"quick and dirty\" joint genotyping on one or more samples pre-called with HaplotypeCaller",
         programGroup = ShortVariantDiscoveryProgramGroup.class)
 @DocumentedFeature
+@BetaFeature
 public final class GnarlyGenotyper extends VariantWalker {
 
     private static final OneShotLogger warning = new OneShotLogger(GnarlyGenotyper.class);
@@ -90,13 +93,6 @@ public final class GnarlyGenotyper extends VariantWalker {
 
     public static final int PIPELINE_MAX_ALT_COUNT = 6;
 
-    private static GnarlyGenotyperEngine genotyperEngine;
-
-    private final RMSMappingQuality mqCalculator = RMSMappingQuality.getInstance();
-
-    private final Set<Class<? extends InfoFieldAnnotation>> allASAnnotations = new HashSet<>();
-
-
     @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME,
             doc="File to which variants should be written", optional=false)
     private File outputFile;
@@ -141,7 +137,10 @@ public final class GnarlyGenotyper extends VariantWalker {
     private final DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
 
     private VariantContextWriter vcfWriter;
-    private VariantContextWriter annotationDBwriter = null;
+    private VariantContextWriter annotationDatabaseWriter = null;
+    private GnarlyGenotyperEngine genotyperEngine;
+    private final RMSMappingQuality mqCalculator = RMSMappingQuality.getInstance();
+    private final Set<Class<? extends InfoFieldAnnotation>> allAlleleSpecificAnnotations = new HashSet<>();
 
     /** these are used when {@link #onlyOutputCallsStartingInIntervals) is true */
     private List<SimpleInterval> intervals;
@@ -194,10 +193,10 @@ public void onTraversalStart() {
 
         Reflections reflections = new Reflections("org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific");
         //not InfoFieldAnnotation.class because we don't want AS_InbreedingCoeff
-        allASAnnotations.addAll(reflections.getSubTypesOf(AS_StrandBiasTest.class));
-        allASAnnotations.addAll(reflections.getSubTypesOf(AS_RankSumTest.class));
-        allASAnnotations.add(AS_RMSMappingQuality.class);
-        allASAnnotations.add(AS_QualByDepth.class);
+        allAlleleSpecificAnnotations.addAll(reflections.getSubTypesOf(AS_StrandBiasTest.class));
+        allAlleleSpecificAnnotations.addAll(reflections.getSubTypesOf(AS_RankSumTest.class));
+        allAlleleSpecificAnnotations.add(AS_RMSMappingQuality.class);
+        allAlleleSpecificAnnotations.add(AS_QualByDepth.class);
     }
 
     private void setupVCFWriter(VCFHeader inputVCFHeader, SampleList samples) {
@@ -230,7 +229,7 @@ private void setupVCFWriter(VCFHeader inputVCFHeader, SampleList samples) {
 
         vcfWriter = createVCFWriter(outputFile);
         if (outputDbName != null) {
-            annotationDBwriter = createVCFWriter(new File(outputDbName));
+            annotationDatabaseWriter = createVCFWriter(new File(outputDbName));
         }
 
         final Set<String> sampleNameSet = samples.asSetOfSamples();
@@ -243,7 +242,7 @@ private void setupVCFWriter(VCFHeader inputVCFHeader, SampleList samples) {
         final VCFHeader vcfHeader = new VCFHeader(headerLines, new TreeSet<>(sampleNameSet));
         vcfWriter.writeHeader(vcfHeader);
         if (outputDbName != null) {
-            annotationDBwriter.writeHeader(dbHeader);
+            annotationDatabaseWriter.writeHeader(dbHeader);
         }
     }
 
@@ -271,12 +270,12 @@ public void apply(VariantContext variant, ReadsContext reads, ReferenceContext r
         }
 
         final VariantContextBuilder annotationDBBuilder = new VariantContextBuilder(variant);
-        final VariantContext finalizedVC = GnarlyGenotyperEngine.finalizeGenotype(variant, annotationDBBuilder);
+        final VariantContext finalizedVC = genotyperEngine.finalizeGenotype(variant, annotationDBBuilder);
         if (finalizedVC != null && (!onlyOutputCallsStartingInIntervals || intervals.stream().anyMatch(interval -> interval.contains(variantStart)))) {
             vcfWriter.add(finalizedVC);
         }
-        if (annotationDBwriter != null) {
-            annotationDBwriter.add(annotationDBBuilder.make());  //we don't seem to have a sites-only option anymore, so do it manually
+        if (annotationDatabaseWriter != null) {
+            annotationDatabaseWriter.add(annotationDBBuilder.make());  //we don't seem to have a sites-only option anymore, so do it manually
         }
     }
 
@@ -285,8 +284,8 @@ public void closeTool() {
         if ( vcfWriter != null) {
             vcfWriter.close();
         }
-        if (annotationDBwriter != null) {
-            annotationDBwriter.close();
+        if (annotationDatabaseWriter != null) {
+            annotationDatabaseWriter.close();
         }
     }
 }
\ No newline at end of file
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java
index a0807fdedc2..70e2f52a98b 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java
@@ -15,16 +15,13 @@
 import java.util.*;
 
 public final class AnnotationUtils {
-    public static final String ALLELE_SPECIFIC_SPLIT_DELIM = "\\|"; //String.split takes a regex, so we need to escape the pipe
     public static final String ALLELE_SPECIFIC_PRINT_DELIM = "|";
     public static final String ALLELE_SPECIFIC_REDUCED_DELIM = ",";
-
-    private AnnotationUtils(){}
-
+    public static final String ALLELE_SPECIFIC_SPLIT_REGEX = "\\|"; //String.split takes a regex, so we need to escape the pipe
+    public static final String BRACKET_REGEX = "\\[|\\]";
     public static final String LIST_DELIMITER = ",";
 
-    public static final String AS_SPLIT_REGEX = "\\|"; //String.split takes a regex, so we need to escape the pipe
-    public static final String PRINT_DELIM = "|";
+    private AnnotationUtils(){}
 
     /**
      * Helper function to parse the list into the annotation string
@@ -54,7 +51,7 @@ public static String encodeStringList( final List<String> stringList) {
      * @return a comma-separated String
      */
     public static String encodeAnyASList( final List<?> somethingList) {
-        return StringUtils.join(somethingList, ALLELE_SPECIFIC_PRINT_DELIM).replaceAll("\\[|\\]", "");  //Who actually wants brackets at the ends of their string?  Who???
+        return StringUtils.join(somethingList, ALLELE_SPECIFIC_PRINT_DELIM).replaceAll(BRACKET_REGEX, "");  //Who actually wants brackets at the ends of their string?  Who???
     }
 
     /**
@@ -90,6 +87,6 @@ public static List<String> getAlleleLengthListOfString(String rawDataString) {
         if (rawDataString.startsWith("[")) {
             rawDataString = rawDataString.substring(1, rawDataString.length() - 1).replaceAll("\\s", "");
         }
-        return Arrays.asList(rawDataString.split(ALLELE_SPECIFIC_SPLIT_DELIM));
+        return Arrays.asList(rawDataString.split(ALLELE_SPECIFIC_SPLIT_REGEX));
     }
 }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java
index 2ee46af62bf..b7d7c979e33 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java
@@ -55,6 +55,7 @@ public final class RMSMappingQuality extends InfoFieldAnnotation implements Stan
     private static final int NUM_LIST_ENTRIES = 2;
     private static final int SUM_OF_SQUARES_INDEX = 0;
     private static final int TOTAL_DEPTH_INDEX = 1;
+    private static final String OUTPUT_PRECISION = "%.2f";
 
     @Override
     public String getRawKeyName() { return GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY;}   //new key for the two-value MQ data to prevent version mismatch catastrophes
@@ -126,10 +127,10 @@ public Map<String, Object> finalizeRawData(final VariantContext vc, final Varian
         else if (vc.hasAttribute(getDeprecatedRawKeyName())) {
             rawMQdata = vc.getAttributeAsString(getDeprecatedRawKeyName(), null);
             //the original version of ReblockGVCF produces a different MQ format -- try to handle that gracefully here just in case those files go through GenotypeGVCFs
-            if (vc.hasAttribute("MQ_DP")) {
-                logger.warn("Presence of MQ_DP key indicates that this tool may be running on an older output of ReblockGVCF " +
+            if (vc.hasAttribute(GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED)) {
+                logger.warn("Presence of " + GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED + " key indicates that this tool may be running on an older output of ReblockGVCF " +
                         "that may not have compatible annotations with this GATK version. Attempting to reformat MQ data.");
-                final String rawMQdepth = vc.getAttributeAsString("MQ_DP",null);
+                final String rawMQdepth = vc.getAttributeAsString(GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED,null);
                 if (rawMQdepth == null) {
                     throw new UserException.BadInput("MQ annotation data is not properly formatted. This version expects a " +
                             "long tuple of sum of squared MQ values and total reads over variant genotypes.");
@@ -159,7 +160,7 @@ else if (vc.hasAttribute(getDeprecatedRawKeyName())) {
     }
 
     private String makeFinalizedAnnotationString(final long numOfReads, final long sumOfSquaredMQs) {
-        return String.format("%.2f", Math.sqrt(sumOfSquaredMQs/(double)numOfReads));
+        return String.format(OUTPUT_PRECISION, Math.sqrt(sumOfSquaredMQs/(double)numOfReads));
     }
 
 
@@ -216,7 +217,7 @@ public Map<String, Object> annotate(final ReferenceContext ref,
 
     @VisibleForTesting
     static String formattedValue(double rms) {
-        return String.format("%.2f", rms);
+        return String.format(OUTPUT_PRECISION, rms);
     }
 
     /**
@@ -229,11 +230,11 @@ static String formattedValue(double rms) {
     public VariantContext finalizeRawMQ(final VariantContext vc) {
         final String rawMQdata = vc.getAttributeAsString(getRawKeyName(), null);
         if (rawMQdata == null) {
-            if (!vc.hasAttribute(GATKVCFConstants.MAPPING_QUALITY_DEPTH)) {
+            if (!vc.hasAttribute(GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED)) {
                 return vc;
             }
-            if (vc.hasAttribute(GATKVCFConstants.MAPPING_QUALITY_DEPTH)) {
-                final int numOfReads = vc.getAttributeAsInt(GATKVCFConstants.MAPPING_QUALITY_DEPTH, getNumOfReads(vc));  //MQ_DP is an undocumented hack for the Gnarly Pipeline -- improved version uses RAW_MQ_and_DP tuple format (see #4969)
+            if (vc.hasAttribute(GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED)) {
+                final int numOfReads = vc.getAttributeAsInt(GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED, getNumOfReads(vc));  //MQ_DP is an undocumented hack for the Gnarly Pipeline -- improved version uses RAW_MQ_and_DP tuple format (see #4969)
                 final String deprecatedRawMQdata = vc.getAttributeAsString(getDeprecatedRawKeyName(), null);
                 final double squareSum = parseDeprecatedRawDataString(deprecatedRawMQdata);
                 final double rms = Math.sqrt(squareSum / (double)numOfReads);
@@ -265,7 +266,7 @@ private void parseRawDataString(ReducibleAnnotationData<List<Long>> myData) {
     //TODO once the AS annotations have been added genotype gvcfs this can be removed for a more generic approach
     private static List<Long> parseRawDataString(String rawDataString) {
         try {
-            final String[] parsed = rawDataString.trim().replaceAll("\\[|\\]", "").split(", *");
+            final String[] parsed = rawDataString.trim().replaceAll(AnnotationUtils.BRACKET_REGEX, "").split(", *");
             if (parsed.length != NUM_LIST_ENTRIES) {
                 throw new UserException.BadInput("Raw value for annotation has " + parsed.length + " values, expected " + NUM_LIST_ENTRIES);
             }
@@ -300,8 +301,8 @@ private static double parseDeprecatedRawDataString(String rawDataString) {
      */
     @VisibleForTesting
     private static int getNumOfReads(final VariantContext vc) {
-        if(vc.hasAttribute(GATKVCFConstants.MAPPING_QUALITY_DEPTH)) {
-            int mqDP = vc.getAttributeAsInt(GATKVCFConstants.MAPPING_QUALITY_DEPTH, 0);
+        if(vc.hasAttribute(GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED)) {
+            int mqDP = vc.getAttributeAsInt(GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED, 0);
             if (mqDP > 0) {
                 return mqDP;
             }
@@ -356,9 +357,9 @@ private static boolean hasReferenceDepth(Genotype gt) {
     static long getNumOfReads(final VariantContext vc,
                              final ReadLikelihoods<Allele> likelihoods) {
         if(vc.hasAttribute(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY)) {
-            List<Long> MQtuple = getAttributeAsLongList(vc, GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY,0L);
-            if (MQtuple.get(TOTAL_DEPTH_INDEX) > 0) {
-                return MQtuple.get(TOTAL_DEPTH_INDEX);
+            List<Long> mqTuple = getAttributeAsLongList(vc, GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY,0L);
+            if (mqTuple.get(TOTAL_DEPTH_INDEX) > 0) {
+                return mqTuple.get(TOTAL_DEPTH_INDEX);
             }
         }
 
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java
index 9db775d10c5..42066f1eecd 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java
@@ -120,7 +120,7 @@ public Map<String, Object> finalizeRawData(VariantContext vc, VariantContext ori
         final List<Integer> standardDepth;
         if (originalVC.hasAttribute(GATKVCFConstants.AS_VARIANT_DEPTH_KEY)) {
             standardDepth = Arrays.stream(originalVC.getAttributeAsString(GATKVCFConstants.AS_VARIANT_DEPTH_KEY, "")
-                    .split(AnnotationUtils.AS_SPLIT_REGEX)).mapToInt(Integer::parseInt).boxed().collect(Collectors.toList());
+                    .split(AnnotationUtils.ALLELE_SPECIFIC_SPLIT_REGEX)).mapToInt(Integer::parseInt).boxed().collect(Collectors.toList());
         } else {
             standardDepth = getAlleleDepths(genotypes);
         }
@@ -192,7 +192,7 @@ public static String finalizeRawGVCFVarDPValues(final String rawAnnotationListWi
         if (rawAnnotationListWithNonRef == null) {
             return null;
         }
-        List<String> dpValues = Arrays.asList(rawAnnotationListWithNonRef.split(AnnotationUtils.AS_SPLIT_REGEX));
+        List<String> dpValues = Arrays.asList(rawAnnotationListWithNonRef.split(AnnotationUtils.ALLELE_SPECIFIC_SPLIT_REGEX));
         if (dpValues.size() != expectedFinalAlleleCount + 1) {  //we expect a nonRef allele
             return null;
         }
@@ -216,7 +216,7 @@ public static List<Integer> parseQualList(final VariantContext vc) {
         }
         else if (vc.hasAttribute(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY)) {
             String asQuals = vc.getAttributeAsString(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY, "").replaceAll("\\[\\]\\s","");
-            String[] values = asQuals.split(AnnotationUtils.AS_SPLIT_REGEX);
+            String[] values = asQuals.split(AnnotationUtils.ALLELE_SPECIFIC_SPLIT_REGEX);
             if (values.length != vc.getNAlleles()+1) {  //plus one because the non-ref place holder is still around
                 throw new IllegalStateException("Number of AS_QUALapprox values doesn't match the number of alleles in the variant context.");
             }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RMSMappingQuality.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RMSMappingQuality.java
index 386e3b1616e..5eaf0ed8d28 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RMSMappingQuality.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RMSMappingQuality.java
@@ -139,7 +139,7 @@ public void combineAttributeMap(final ReducibleAnnotationData<Double> toAdd, fin
     protected void parseRawDataString(final ReducibleAnnotationData<Double> myData) {
         final String rawDataString = myData.getRawData();
         //get per-allele data by splitting on allele delimiter
-        final String[] rawDataPerAllele = rawDataString.split(AnnotationUtils.AS_SPLIT_REGEX);
+        final String[] rawDataPerAllele = rawDataString.split(AnnotationUtils.ALLELE_SPECIFIC_SPLIT_REGEX);
         for (int i=0; i<rawDataPerAllele.length; i++) {
             final String alleleData = rawDataPerAllele[i];
             myData.putAttribute(myData.getAlleles().get(i), Double.parseDouble(alleleData));
@@ -196,7 +196,7 @@ private String makeRawAnnotationString(final List<Allele> vcAlleles, final Map<A
         String annotationString = "";
         for (final Allele current : vcAlleles) {
             if (!annotationString.isEmpty()) {
-                annotationString += AnnotationUtils.PRINT_DELIM;
+                annotationString += AnnotationUtils.ALLELE_SPECIFIC_PRINT_DELIM;
             }
             if(perAlleleValues.get(current) != null) {
                 annotationString += String.format(printFormat, perAlleleValues.get(current));
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RankSumTest.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RankSumTest.java
index bd7ab34f1dc..77559e6197f 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RankSumTest.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_RankSumTest.java
@@ -250,7 +250,7 @@ protected void parseRawDataString(final ReducibleAnnotationData<Histogram> myDat
         }
         //TODO handle misformatted annotation field more gracefully
         //rawDataPerAllele is a per-sample list of the rank sum statistic for each allele
-        final String[] rawDataPerAllele = rawDataNoBrackets.split(AnnotationUtils.ALLELE_SPECIFIC_SPLIT_DELIM);
+        final String[] rawDataPerAllele = rawDataNoBrackets.split(AnnotationUtils.ALLELE_SPECIFIC_SPLIT_REGEX);
         for (int i=0; i<rawDataPerAllele.length; i++) {
             final String alleleData = rawDataPerAllele[i];
             final Histogram alleleList = perAlleleValues.get(myData.getAlleles().get(i));
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
index bce8c5c1e41..4aabb81dc91 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
@@ -174,7 +174,7 @@ public void onTraversalStart() {
         headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_VARIANT_DEPTH_KEY));
         headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RAW_GENOTYPE_COUNT_KEY));
         headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY));
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MAPPING_QUALITY_DEPTH));  //NOTE: this is deprecated, but keep until we reprocess all GVCFs
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED));  //NOTE: this is deprecated, but keep until we reprocess all GVCFs
         if (inputHeader.hasInfoLine(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY)) {
             headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY));  //NOTE: this is deprecated, but keep until we reprocess all GVCFs
         }
@@ -456,7 +456,7 @@ protected VariantContext cleanUpHighQualityVariant(final VariantContext result,
                             originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0));
             attrMap.put(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY,
                     String.format("%d,%d", rawMqValue, originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0)));
-            attrMap.put(GATKVCFConstants.MAPPING_QUALITY_DEPTH, originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0)); //NOTE: this annotation is deprecated, but keep it here so we don't have to reprocess gnomAD v3 GVCFs again
+            attrMap.put(GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED, originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0)); //NOTE: this annotation is deprecated, but keep it here so we don't have to reprocess gnomAD v3 GVCFs again
             if (originalVC.hasAttribute(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY)) {
                 attrMap.put(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY, originalVC.getAttributeAsDouble(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY, 0)); //NOTE: this annotation is deprecated, but keep it here so we don't have to reprocess gnomAD v3 GVCFs again
             }
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java
index 88c63cef289..478ab4456ed 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java
@@ -33,13 +33,13 @@ public static GenotypeCounts computeDiploidGenotypeCounts(final VariantContext v
         Utils.nonNull(vc, "vc");
         Utils.nonNull(genotypes, "genotypes");
 
-        int idxAA = 0;
-        int idxAB = 1;
-        int idxBB = 2;
+        final int idxAA = 0;
+        final int idxAB = 1;
+        final int idxBB = 2;
 
-        double refCount = 0;
-        double hetCount = 0;
-        double varCount = 0;
+        double genotypeWithTwoRefsCount = 0;  //i.e. 0/0
+        double genotypesWithOneRefCount = 0;  //e.g. 0/1, 0/2, etc.
+        double genotypesWithNoRefsCount = 0;  //e.g. 1/1, 1/2, 2/2, etc.
 
         for (final Genotype g : genotypes) {
             if (! isDiploidWithLikelihoods(g)){
@@ -56,8 +56,8 @@ public static GenotypeCounts computeDiploidGenotypeCounts(final VariantContext v
                 int maxInd = MathUtil.indexOfMax(normalizedLikelihoods);
                 GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(maxInd);
                 if (alleles.alleleIndex1 != 0 && alleles.alleleIndex2 != 0) {
-                    //all likelihoods go to varCount because no ref allele is called
-                    varCount++;
+                    //all likelihoods go to genotypesWithNoRefsCount because no ref allele is called
+                    genotypesWithNoRefsCount++;
                     continue;
                 }
 
@@ -85,19 +85,19 @@ public static GenotypeCounts computeDiploidGenotypeCounts(final VariantContext v
 
             //NOTE: rounding is special cased for [0,0,X] and [X,0,0] PLs because likelihoods can come out as [0.5, 0.5, 0] and both counts round up
             if( roundContributionFromEachGenotype ) {
-                refCount += MathUtils.fastRound(refLikelihood);
+                genotypeWithTwoRefsCount += MathUtils.fastRound(refLikelihood);
                 if (refLikelihood != hetLikelihood) {   //if GQ = 0 (specifically [0,0,X] PLs) count as homRef and don't add to the other counts
-                    hetCount += MathUtils.fastRound(hetLikelihood);
+                    genotypesWithOneRefCount += MathUtils.fastRound(hetLikelihood);
                 }
                 if (varLikelihood != hetLikelihood) {  //if GQ = 0 (specifically [X,0,0] PLs) count as het and don't count as variant
-                    varCount += MathUtils.fastRound(varLikelihood); //need specific varCount (rather than complement of the others) for PL[0,0,0] case
+                    genotypesWithNoRefsCount += MathUtils.fastRound(varLikelihood); //need specific genotypesWithNoRefsCount (rather than complement of the others) for PL[0,0,0] case
                 }
             } else {
-                refCount += refLikelihood;
-                hetCount += hetLikelihood;
-                varCount += varLikelihood;
+                genotypeWithTwoRefsCount += refLikelihood;
+                genotypesWithOneRefCount += hetLikelihood;
+                genotypesWithNoRefsCount += varLikelihood;
             }
         }
-        return new GenotypeCounts(refCount, hetCount, varCount);
+        return new GenotypeCounts(genotypeWithTwoRefsCount, genotypesWithOneRefCount, genotypesWithNoRefsCount);
     }
 }
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
index 2d3ea3b0d65..39d6df880be 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
@@ -20,7 +20,7 @@ public final class GATKVCFConstants {
     public static final String ALLELE_SPECIFIC_PREFIX =             "AS_";
     public static final String AS_FILTER_STATUS_KEY =               "AS_FilterStatus";
     public static final String RAW_RMS_MAPPING_QUALITY_KEY =        "RAW_MQ";
-    public static final String MAPPING_QUALITY_DEPTH =              "MQ_DP";  //NOTE: this is deprecated in favor of the new RAW_MQandDP below
+    public static final String MAPPING_QUALITY_DEPTH_DEPRECATED =   "MQ_DP";  //NOTE: this is deprecated in favor of the new RAW_MQandDP below
     public static final String RAW_MAPPING_QUALITY_WITH_DEPTH_KEY = "RAW_MQandDP";
     public static final String AS_RMS_MAPPING_QUALITY_KEY =         "AS_MQ";
     public static final String AS_RAW_RMS_MAPPING_QUALITY_KEY =     "AS_RAW_MQ";
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java
index 2f68547bcde..56791213c0c 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java
@@ -160,7 +160,7 @@ public static VCFFormatHeaderLine getEquivalentFormatHeaderLine(final String inf
         addInfoLine(new VCFInfoHeaderLine(LIKELIHOOD_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref haplotype likelihoods"));
         addInfoLine(new VCFInfoHeaderLine(MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"));
         addInfoLine(new VCFInfoHeaderLine(AS_MAP_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific Z-score From Wilcoxon rank sum test of each Alt vs. Ref read mapping qualities"));
-        addInfoLine(new VCFInfoHeaderLine(MAPPING_QUALITY_DEPTH, 1, VCFHeaderLineType.Integer, "Depth over variant samples for better MQ calculation (deprecated -- use " + RAW_MAPPING_QUALITY_WITH_DEPTH_KEY + " instead."));
+        addInfoLine(new VCFInfoHeaderLine(MAPPING_QUALITY_DEPTH_DEPRECATED, 1, VCFHeaderLineType.Integer, "Depth over variant samples for better MQ calculation (deprecated -- use " + RAW_MAPPING_QUALITY_WITH_DEPTH_KEY + " instead."));
         addInfoLine(new VCFInfoHeaderLine(RAW_RMS_MAPPING_QUALITY_KEY, 1, VCFHeaderLineType.Integer, "Raw data for RMS Mapping Quality (deprecated -- use " + RAW_MAPPING_QUALITY_WITH_DEPTH_KEY + " instead."));
         addInfoLine(new VCFInfoHeaderLine(RAW_MAPPING_QUALITY_WITH_DEPTH_KEY, 2, VCFHeaderLineType.Integer, "Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated " + RMSMappingQuality.getDeprecatedRawKeyName() + " formulation."));
         addInfoLine(new VCFInfoHeaderLine(AS_RAW_RMS_MAPPING_QUALITY_KEY, 1, VCFHeaderLineType.String, "Allele-specfic raw data for RMS Mapping Quality"));
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java
index 322aca23627..2a8e8e72ad5 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java
@@ -171,7 +171,7 @@ public void testLikelihoods_AS(){
         Assert.assertEquals(annotate.size(), 1, "size");
         Assert.assertEquals(annotate.keySet(), Collections.singleton(GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY), "annots");
         final double rms= MathUtils.sumOfSquares(MQsListOK); //only those are MQ0
-        final String[] split =((String)annotate.get(GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY)).split(AnnotationUtils.AS_SPLIT_REGEX);
+        final String[] split =((String)annotate.get(GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY)).split(AnnotationUtils.ALLELE_SPECIFIC_SPLIT_REGEX);
         Assert.assertEquals(split.length, 2);
         Assert.assertEquals(split[0], String.format("%.2f", rms));
         Assert.assertEquals(split[1], String.format("%.2f", 0.0));
@@ -188,7 +188,7 @@ public void testLikelihoodsEmpty_AS() throws Exception {
         final VariantContext vc= makeVC();
         final ReferenceContext referenceContext= null;
         final Map<String, Object> annotate = new AS_RMSMappingQuality().annotateRawData(referenceContext, vc, likelihoods);
-        final String[] split =((String)annotate.get(GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY)).split(AnnotationUtils.AS_SPLIT_REGEX);
+        final String[] split =((String)annotate.get(GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY)).split(AnnotationUtils.ALLELE_SPECIFIC_SPLIT_REGEX);
         Assert.assertEquals(split.length, 2);
         Assert.assertEquals(split[0], String.format("%.2f", 0.0));
         Assert.assertEquals(split[1], String.format("%.2f", 0.0));
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.keepRawCombined.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.keepRawCombined.expected.vcf
index ff755f200f3..20cf82bdbc0 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.keepRawCombined.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.keepRawCombined.expected.vcf
@@ -12,7 +12,7 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.7-43-gc7dbd4f,Date="Tue Jun 27 08:39:50 EDT 2017",Epoch=1498567190652,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/Users/gauthier/workspaces/gsa-unstable/private/gatk-tools-private/src/test/resources//NA12878.HiSeq.b37.chr20.10_11mb.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[20:10433000-10437000, 20:10087820, 20:10684106] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, AS_Standard] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genotypegvcf6548421458413427550.vcf --keep-combined-raw-annotations true --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12878.AS.chr20snippet.g.vcf --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR --annotation ClippingRankSumTest --annotation-group AS_StandardAnnotation --annotation-group StandardAnnotation  --include-non-variant-sites false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="March 22, 2019 4:41:53 PM EDT">
+##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genotypegvcf1543970441561743372.vcf --keep-combined-raw-annotations true --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12878.AS.chr20snippet.g.vcf --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR --annotation ClippingRankSumTest --annotation-group AS_StandardAnnotation --annotation-group StandardAnnotation  --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="Unavailable",Date="July 22, 2019 3:18:51 PM EDT">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -47,6 +47,7 @@
 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
 ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RAW_GT_COUNT,Number=3,Type=Integer,Description="Counts of genotypes w.r.t. the reference allele: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity">
 ##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
 ##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
@@ -139,27 +140,27 @@
 ##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
 ##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	10087820	.	C	CAG	294.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.100;AS_FS=2.811;AS_MQ=60.00;AS_MQRankSum=0.600;AS_QD=6.14;AS_QUAL=-2.946e+01;AS_RAW_BaseQRankSum=||-2.1,1;AS_RAW_MQ=123769.00|3600.00|46800.00;AS_RAW_MQRankSum=||0.6,1;AS_RAW_ReadPosRankSum=||-0.4,1;AS_ReadPosRankSum=-0.400;AS_SB_TABLE=17,18|1,0|8,5;AS_SOR=1.147;BaseQRankSum=-2.273e+00;DP=93;ExcessHet=3.0103;FS=4.432;MLEAC=1;MLEAF=0.500;MQ=59.55;MQRankSum=0.678;QD=6.14;RAW_MQ=329810.00;ReadPosRankSum=-4.920e-01;SOR=1.302	GT:AD:GQ:PL	0/1:35,13:99:302,0,1079
-20	10433322	.	A	AT	116.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.500;AS_FS=0.000;AS_MQ=44.10;AS_MQRankSum=1.100;AS_QD=7.29;AS_QUAL=-1.166e+01;AS_RAW_BaseQRankSum=|2.5,1;AS_RAW_MQ=14418.00|9723.00;AS_RAW_MQRankSum=|1.1,1;AS_RAW_ReadPosRankSum=|2.0,1;AS_ReadPosRankSum=2.000;AS_SB_TABLE=5,6|2,3;AS_SOR=0.836;BaseQRankSum=2.56;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=43.98;MQRankSum=1.12;QD=7.29;RAW_MQ=67710.00;ReadPosRankSum=2.04;SOR=0.836	GT:AD:GQ:PL	0/1:11,5:99:124,0,369
-20	10433324	.	A	T	220.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.200;AS_FS=0.000;AS_MQ=41.96;AS_MQRankSum=0.500;AS_QD=15.76;AS_QUAL=-2.206e+01;AS_RAW_BaseQRankSum=|2.2,1;AS_RAW_MQ=11895.00|10564.00;AS_RAW_MQRankSum=|0.5,1;AS_RAW_ReadPosRankSum=|1.5,1;AS_ReadPosRankSum=1.500;AS_SB_TABLE=2,6|2,4;AS_SOR=0.412;BaseQRankSum=2.28;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=42.82;MQRankSum=0.584;QD=15.76;RAW_MQ=60510.00;ReadPosRankSum=1.54;SOR=0.412	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275
-20	10433326	.	A	T	220.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.800;AS_FS=0.000;AS_MQ=41.96;AS_MQRankSum=0.500;AS_QD=15.76;AS_QUAL=-2.206e+01;AS_RAW_BaseQRankSum=|0.8,1;AS_RAW_MQ=11895.00|10564.00;AS_RAW_MQRankSum=|0.5,1;AS_RAW_ReadPosRankSum=|1.4,1;AS_ReadPosRankSum=1.400;AS_SB_TABLE=2,6|2,4;AS_SOR=0.412;BaseQRankSum=0.874;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.47;MQRankSum=0.584;QD=15.76;RAW_MQ=53310.00;ReadPosRankSum=1.40;SOR=0.412	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275
-20	10433328	.	A	T,ATATAT	902.06	.	AC=1,1;AF=0.500,0.500;AN=2;AS_BaseQRankSum=nul,nul;AS_FS=0.000,0.000;AS_MQ=41.96,29.00;AS_MQRankSum=nul,nul;AS_QD=25.36,28.73;AS_QUAL=-3.976e+01,-1.110e+01;AS_RAW_BaseQRankSum=|||||;AS_RAW_MQ=0.00|10564.00|2523.00|0.00|0.00|0.00;AS_RAW_MQRankSum=|||||;AS_RAW_ReadPosRankSum=|||||;AS_ReadPosRankSum=nul,nul;AS_SB_TABLE=0,0|2,4|1,2|0,0|0,0|0,0;AS_SOR=1.329,1.179;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=40.71;QD=30.97;RAW_MQ=49710.00;SOR=1.402	GT:AD:GQ:PL	1/2:0,6,3:99:919,177,246,420,0,500
-20	10433382	.	T	C	624.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.900;AS_FS=0.000;AS_MQ=55.21;AS_MQRankSum=1.000;AS_QD=20.82;AS_QUAL=-6.246e+01;AS_RAW_BaseQRankSum=|-1.9,1;AS_RAW_MQ=40862.00|45723.00;AS_RAW_MQRankSum=|1.0,1;AS_RAW_ReadPosRankSum=|0.2,1;AS_ReadPosRankSum=0.200;AS_SB_TABLE=10,5|11,4;AS_SOR=0.998;BaseQRankSum=-1.821e+00;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=1.03;QD=20.82;RAW_MQ=86585.00;ReadPosRankSum=0.249;SOR=0.998	GT:AD:GQ:PGT:PID:PL	0/1:15,15:99:0|1:10433382_T_C:632,0,601
-20	10433391	.	T	C	623.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.300;AS_FS=0.000;AS_MQ=57.05;AS_MQRankSum=1.300;AS_QD=18.34;AS_QUAL=-6.236e+01;AS_RAW_BaseQRankSum=|-0.3,1;AS_RAW_MQ=51662.00|52082.00;AS_RAW_MQRankSum=|1.3,1;AS_RAW_ReadPosRankSum=|1.5,1;AS_ReadPosRankSum=1.500;AS_SB_TABLE=14,4|13,3;AS_SOR=0.859;BaseQRankSum=-2.840e-01;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.24;MQRankSum=1.33;QD=18.34;RAW_MQ=103744.00;ReadPosRankSum=1.54;SOR=0.859	GT:AD:GQ:PGT:PID:PL	0/1:18,16:99:0|1:10433382_T_C:631,0,673
-20	10433468	.	T	C	645.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=2.955;AS_MQ=58.84;AS_MQRankSum=0.000;AS_QD=16.99;AS_QUAL=-6.456e+01;AS_RAW_BaseQRankSum=|-1.4,1;AS_RAW_MQ=63049.00|69241.00;AS_RAW_MQRankSum=|0.0,1;AS_RAW_ReadPosRankSum=|1.4,1;AS_ReadPosRankSum=1.400;AS_SB_TABLE=13,5|12,8;AS_SOR=0.324;BaseQRankSum=-1.312e+00;DP=38;ExcessHet=3.0103;FS=2.955;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=0.076;QD=16.99;RAW_MQ=132290.00;ReadPosRankSum=1.46;SOR=0.324	GT:AD:GQ:PL	0/1:18,20:99:653,0,572
-20	10433560	.	C	A	987.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.400;AS_FS=5.027;AS_MQ=59.25;AS_MQRankSum=-1.100;AS_QD=17.64;AS_QUAL=-9.876e+01;AS_RAW_BaseQRankSum=|3.4,1;AS_RAW_MQ=111600.00|87769.00;AS_RAW_MQRankSum=|-1.1,1;AS_RAW_ReadPosRankSum=|1.3,1;AS_ReadPosRankSum=1.300;AS_SB_TABLE=30,1|22,3;AS_SOR=0.129;BaseQRankSum=3.50;DP=56;ExcessHet=3.0103;FS=5.027;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=-1.078e+00;QD=17.64;RAW_MQ=199369.00;ReadPosRankSum=1.38;SOR=0.129	GT:AD:GQ:PGT:PID:PL	0/1:31,25:99:0|1:10433560_C_A:995,0,3032
-20	10433575	.	C	T	1143.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.800;AS_FS=1.568;AS_MQ=57.81;AS_MQRankSum=-1.200;AS_QD=17.87;AS_QUAL=-1.144e+02;AS_RAW_BaseQRankSum=|3.8,1;AS_RAW_MQ=119641.00|100251.00;AS_RAW_MQRankSum=|-1.2,1;AS_RAW_ReadPosRankSum=|0.8,1;AS_ReadPosRankSum=0.800;AS_SB_TABLE=31,3|26,4;AS_SOR=0.375;BaseQRankSum=3.81;DP=64;ExcessHet=3.0103;FS=1.568;MLEAC=1;MLEAF=0.500;MQ=58.62;MQRankSum=-1.123e+00;QD=17.87;RAW_MQ=219892.00;ReadPosRankSum=0.830;SOR=0.375	GT:AD:GQ:PGT:PID:PL	0/1:34,30:99:0|1:10433560_C_A:1151,0,3385
-20	10433594	.	C	T	1105.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=4.800;AS_FS=1.535;AS_MQ=54.33;AS_MQRankSum=-2.400;AS_QD=18.43;AS_QUAL=-1.106e+02;AS_RAW_BaseQRankSum=|4.8,1;AS_RAW_MQ=108841.00|85615.00;AS_RAW_MQRankSum=|-2.4,1;AS_RAW_ReadPosRankSum=|-0.6,1;AS_ReadPosRankSum=-0.600;AS_SB_TABLE=28,3|25,4;AS_SOR=0.415;BaseQRankSum=4.82;DP=61;ExcessHet=3.0103;FS=1.535;MLEAC=1;MLEAF=0.500;MQ=56.66;MQRankSum=-2.334e+00;QD=18.43;RAW_MQ=195825.00;ReadPosRankSum=-5.020e-01;SOR=0.415	GT:AD:GQ:PGT:PID:PL	0/1:31,29:99:0|1:10433560_C_A:1113,0,3070
-20	10433809	.	A	G	1135.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.400;AS_FS=0.968;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=17.21;AS_QUAL=-1.136e+02;AS_RAW_BaseQRankSum=|1.4,1;AS_RAW_MQ=115200.00|122400.00;AS_RAW_MQRankSum=|0.0,1;AS_RAW_ReadPosRankSum=|-0.5,1;AS_ReadPosRankSum=-0.500;AS_SB_TABLE=13,19|12,22;AS_SOR=0.930;BaseQRankSum=1.41;DP=68;ExcessHet=3.0103;FS=0.968;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=0.00;QD=17.21;RAW_MQ=242569.00;ReadPosRankSum=-4.450e-01;SOR=0.930	GT:AD:GQ:PL	0/1:32,34:99:1143,0,1041
-20	10433955	.	C	CGTGTGTGTGTAT	1027.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_MQ=40.57;AS_MQRankSum=-4.000;AS_QD=24.47;AS_QUAL=-1.028e+02;AS_RAW_BaseQRankSum=|0.4,1;AS_RAW_MQ=59810.00|39497.00;AS_RAW_MQRankSum=|-4.0,1;AS_RAW_ReadPosRankSum=|-0.8,1;AS_ReadPosRankSum=-0.800;AS_SB_TABLE=12,6|16,8;AS_SOR=0.710;BaseQRankSum=0.422;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.96;MQRankSum=-4.001e+00;QD=24.47;RAW_MQ=117307.00;ReadPosRankSum=-7.890e-01;SOR=0.710	GT:AD:GQ:PL	0/1:18,24:99:1035,0,1217
-20	10434177	.	A	T	1467.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.900;AS_FS=0.888;AS_MQ=55.78;AS_MQRankSum=-2.500;AS_QD=20.10;AS_QUAL=-1.468e+02;AS_RAW_BaseQRankSum=|0.9,1;AS_RAW_MQ=108000.00|133784.00;AS_RAW_MQRankSum=|-2.5,1;AS_RAW_ReadPosRankSum=|-0.9,1;AS_ReadPosRankSum=-0.900;AS_SB_TABLE=15,15|23,20;AS_SOR=0.836;BaseQRankSum=0.903;DP=74;ExcessHet=3.0103;FS=0.888;MLEAC=1;MLEAF=0.500;MQ=57.58;MQRankSum=-2.473e+00;QD=20.10;RAW_MQ=245384.00;ReadPosRankSum=-8.910e-01;SOR=0.836	GT:AD:GQ:PL	0/1:30,43:99:1475,0,936
-20	10434258	.	G	A	1235.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.000;AS_FS=0.000;AS_MQ=52.93;AS_MQRankSum=-2.900;AS_QD=17.91;AS_QUAL=-1.236e+02;AS_RAW_BaseQRankSum=|3.0,1;AS_RAW_MQ=109369.00|106451.00;AS_RAW_MQRankSum=|-2.9,1;AS_RAW_ReadPosRankSum=|-0.2,1;AS_ReadPosRankSum=-0.200;AS_SB_TABLE=19,12|24,14;AS_SOR=0.776;BaseQRankSum=3.06;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.99;MQRankSum=-2.871e+00;QD=17.91;RAW_MQ=219420.00;ReadPosRankSum=-1.550e-01;SOR=0.776	GT:AD:GQ:PL	0/1:31,38:99:1243,0,1003
-20	10434384	.	TA	T	782.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.100;AS_FS=0.000;AS_MQ=60.00;AS_MQRankSum=1.000;AS_QD=11.51;AS_QUAL=-7.826e+01;AS_RAW_BaseQRankSum=|-0.1,1;AS_RAW_MQ=123769.00|118800.00;AS_RAW_MQRankSum=|1.0,1;AS_RAW_ReadPosRankSum=|0.4,1;AS_ReadPosRankSum=0.400;AS_SB_TABLE=22,13|21,12;AS_SOR=0.723;BaseQRankSum=-1.000e-01;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=1.00;QD=11.51;RAW_MQ=253369.00;ReadPosRankSum=0.497;SOR=0.723	GT:AD:GQ:PL	0/1:35,33:99:790,0,846
-20	10434519	.	T	C	1464.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-3.200;AS_FS=1.877;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=18.78;AS_QUAL=-1.465e+02;AS_RAW_BaseQRankSum=|-3.2,1;AS_RAW_MQ=126000.00|154800.00;AS_RAW_MQRankSum=|0.0,1;AS_RAW_ReadPosRankSum=|-0.8,1;AS_ReadPosRankSum=-0.800;AS_SB_TABLE=18,17|19,24;AS_SOR=0.900;BaseQRankSum=-3.137e+00;DP=78;ExcessHet=3.0103;FS=1.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.78;RAW_MQ=280800.00;ReadPosRankSum=-7.490e-01;SOR=0.900	GT:AD:GQ:PL	0/1:35,43:99:1472,0,1192
-20	10435067	.	GTA	G	1446.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.600;AS_FS=3.289;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=21.59;AS_QUAL=-1.447e+02;AS_RAW_BaseQRankSum=|2.6,1;AS_RAW_MQ=108000.00|133200.00;AS_RAW_MQRankSum=|0.0,1;AS_RAW_ReadPosRankSum=|-0.2,1;AS_ReadPosRankSum=-0.200;AS_SB_TABLE=15,15|22,15;AS_SOR=1.121;BaseQRankSum=2.60;DP=67;ExcessHet=3.0103;FS=3.289;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.59;RAW_MQ=241200.00;ReadPosRankSum=-1.830e-01;SOR=1.121	GT:AD:GQ:PL	0/1:30,37:99:1454,0,1191
-20	10435948	.	A	C	1137.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-4.700;AS_FS=3.002;AS_MQ=54.65;AS_MQRankSum=-3.200;AS_QD=14.97;AS_QUAL=-1.138e+02;AS_RAW_BaseQRankSum=|-4.7,1;AS_RAW_MQ=144000.00|107528.00;AS_RAW_MQRankSum=|-3.2,1;AS_RAW_ReadPosRankSum=|-1.6,1;AS_ReadPosRankSum=-1.600;AS_SB_TABLE=19,21|20,16;AS_SOR=0.855;BaseQRankSum=-4.692e+00;DP=76;ExcessHet=3.0103;FS=3.002;MLEAC=1;MLEAF=0.500;MQ=57.53;MQRankSum=-3.121e+00;QD=14.97;RAW_MQ=251528.00;ReadPosRankSum=-1.594e+00;SOR=0.855	GT:AD:GQ:PL	0/1:40,36:99:1145,0,1413
-20	10436227	.	TTTTATTTATTTATTTATTTA	T,TTTTATTTATTTATTTATTTATTTA	1208.06	.	AC=1,1;AF=0.500,0.500;AN=2;AS_BaseQRankSum=nul,nul;AS_FS=0.000,0.000;AS_MQ=32.72,53.03;AS_MQRankSum=nul,nul;AS_QD=27.24,28.88;AS_QUAL=-9.370e+01,-2.310e+01;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=3600.00|25702.00|19682.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_ReadPosRankSum=nul,nul;AS_SB_TABLE=1,0|14,10|4,3;AS_SOR=0.382,0.330;BaseQRankSum=-1.450e+00;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.77;MQRankSum=-1.660e+00;QD=28.20;RAW_MQ=201025.00;ReadPosRankSum=1.30;SOR=0.379	GT:AD:GQ:PL	1/2:1,24,7:99:1225,241,589,947,0,970
-20	10436415	.	A	G	1190.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.800;AS_FS=9.312;AS_MQ=59.42;AS_MQRankSum=0.400;AS_QD=18.90;AS_QUAL=-1.191e+02;AS_RAW_BaseQRankSum=|-2.8,1;AS_RAW_MQ=81904.00|141241.00;AS_RAW_MQRankSum=|0.4,1;AS_RAW_ReadPosRankSum=|-0.1,1;AS_ReadPosRankSum=-0.100;AS_SB_TABLE=15,8|17,23;AS_SOR=0.739;BaseQRankSum=-2.775e+00;DP=63;ExcessHet=3.0103;FS=9.312;MLEAC=1;MLEAF=0.500;MQ=59.51;MQRankSum=0.399;QD=18.90;RAW_MQ=223145.00;ReadPosRankSum=-6.300e-02;SOR=0.739	GT:AD:GQ:PL	0/1:23,40:99:1198,0,691
-20	10436582	.	A	G	1187.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=3.189;AS_MQ=52.86;AS_MQRankSum=-2.700;AS_QD=16.73;AS_QUAL=-1.188e+02;AS_RAW_BaseQRankSum=|-1.4,1;AS_RAW_MQ=117410.00|103379.00;AS_RAW_MQRankSum=|-2.7,1;AS_RAW_ReadPosRankSum=|0.2,1;AS_ReadPosRankSum=0.200;AS_SB_TABLE=16,18|21,16;AS_SOR=0.906;BaseQRankSum=-1.326e+00;DP=71;ExcessHet=3.0103;FS=3.189;MLEAC=1;MLEAF=0.500;MQ=55.76;MQRankSum=-2.639e+00;QD=16.73;RAW_MQ=220789.00;ReadPosRankSum=0.267;SOR=0.906	GT:AD:GQ:PL	0/1:34,37:99:1195,0,1113
-20	10436700	.	A	G	1333.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=2.012;AS_MQ=59.53;AS_MQRankSum=-0.900;AS_QD=19.05;AS_QUAL=-1.334e+02;AS_RAW_BaseQRankSum=|-1.4,1;AS_RAW_MQ=108000.00|141769.00;AS_RAW_MQRankSum=|-0.9,1;AS_RAW_ReadPosRankSum=|0.5,1;AS_ReadPosRankSum=0.500;AS_SB_TABLE=18,12|21,19;AS_SOR=0.449;BaseQRankSum=-1.329e+00;DP=70;ExcessHet=3.0103;FS=2.012;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-8.370e-01;QD=19.05;RAW_MQ=249769.00;ReadPosRankSum=0.581;SOR=0.449	GT:AD:GQ:PL	0/1:30,40:99:1341,0,961
-20	10436908	.	C	G	1361.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.900;AS_FS=4.557;AS_MQ=58.89;AS_MQRankSum=-1.000;AS_QD=16.40;AS_QUAL=-1.362e+02;AS_RAW_BaseQRankSum=|-0.9,1;AS_RAW_MQ=145849.00|145638.00;AS_RAW_MQRankSum=|-1.0,1;AS_RAW_ReadPosRankSum=|-0.2,1;AS_ReadPosRankSum=-0.200;AS_SB_TABLE=15,26|11,31;AS_SOR=1.252;BaseQRankSum=-8.440e-01;DP=83;ExcessHet=3.0103;FS=4.557;MLEAC=1;MLEAF=0.500;MQ=59.26;MQRankSum=-9.940e-01;QD=16.40;RAW_MQ=291487.00;ReadPosRankSum=-1.480e-01;SOR=1.252	GT:AD:GQ:PL	0/1:41,42:99:1369,0,1378
+20	10087820	.	C	CAG	294.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.100;AS_FS=2.811;AS_MQ=60.00;AS_MQRankSum=0.600;AS_RAW_BaseQRankSum=||-2.1,1;AS_RAW_MQ=123769.00|3600.00|46800.00;AS_RAW_MQRankSum=||0.6,1;AS_RAW_ReadPosRankSum=||-0.4,1;AS_ReadPosRankSum=-0.400;AS_SB_TABLE=17,18|1,0|8,5;AS_SOR=1.147;BaseQRankSum=-2.273e+00;DP=93;ExcessHet=3.0103;FS=4.432;MLEAC=1;MLEAF=0.500;MQ=59.55;MQRankSum=0.678;QD=6.14;RAW_MQ=329810.00;ReadPosRankSum=-4.920e-01;SOR=1.302	GT:AD:GQ:PL	0/1:35,13:99:302,0,1079
+20	10433322	.	A	AT	116.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.500;AS_FS=0.000;AS_MQ=44.10;AS_MQRankSum=1.100;AS_RAW_BaseQRankSum=|2.5,1;AS_RAW_MQ=14418.00|9723.00;AS_RAW_MQRankSum=|1.1,1;AS_RAW_ReadPosRankSum=|2.0,1;AS_ReadPosRankSum=2.000;AS_SB_TABLE=5,6|2,3;AS_SOR=0.836;BaseQRankSum=2.56;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=43.98;MQRankSum=1.12;QD=7.29;RAW_MQ=67710.00;ReadPosRankSum=2.04;SOR=0.836	GT:AD:GQ:PL	0/1:11,5:99:124,0,369
+20	10433324	.	A	T	220.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.200;AS_FS=0.000;AS_MQ=41.96;AS_MQRankSum=0.500;AS_RAW_BaseQRankSum=|2.2,1;AS_RAW_MQ=11895.00|10564.00;AS_RAW_MQRankSum=|0.5,1;AS_RAW_ReadPosRankSum=|1.5,1;AS_ReadPosRankSum=1.500;AS_SB_TABLE=2,6|2,4;AS_SOR=0.412;BaseQRankSum=2.28;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=42.82;MQRankSum=0.584;QD=15.76;RAW_MQ=60510.00;ReadPosRankSum=1.54;SOR=0.412	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275
+20	10433326	.	A	T	220.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.800;AS_FS=0.000;AS_MQ=41.96;AS_MQRankSum=0.500;AS_RAW_BaseQRankSum=|0.8,1;AS_RAW_MQ=11895.00|10564.00;AS_RAW_MQRankSum=|0.5,1;AS_RAW_ReadPosRankSum=|1.4,1;AS_ReadPosRankSum=1.400;AS_SB_TABLE=2,6|2,4;AS_SOR=0.412;BaseQRankSum=0.874;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.47;MQRankSum=0.584;QD=15.76;RAW_MQ=53310.00;ReadPosRankSum=1.40;SOR=0.412	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275
+20	10433328	.	A	T,ATATAT	902.06	.	AC=1,1;AF=0.500,0.500;AN=2;AS_BaseQRankSum=nul,nul;AS_FS=0.000,0.000;AS_MQ=41.96,29.00;AS_MQRankSum=nul,nul;AS_RAW_BaseQRankSum=|||||;AS_RAW_MQ=0.00|10564.00|2523.00|0.00|0.00|0.00;AS_RAW_MQRankSum=|||||;AS_RAW_ReadPosRankSum=|||||;AS_ReadPosRankSum=nul,nul;AS_SB_TABLE=0,0|2,4|1,2|0,0|0,0|0,0;AS_SOR=1.329,1.179;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=40.71;QD=25.36;RAW_MQ=49710.00;SOR=1.402	GT:AD:GQ:PL	1/2:0,6,3:99:919,177,246,420,0,500
+20	10433382	.	T	C	624.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.900;AS_FS=0.000;AS_MQ=55.21;AS_MQRankSum=1.000;AS_RAW_BaseQRankSum=|-1.9,1;AS_RAW_MQ=40862.00|45723.00;AS_RAW_MQRankSum=|1.0,1;AS_RAW_ReadPosRankSum=|0.2,1;AS_ReadPosRankSum=0.200;AS_SB_TABLE=10,5|11,4;AS_SOR=0.998;BaseQRankSum=-1.821e+00;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=1.03;QD=20.82;RAW_MQ=86585.00;ReadPosRankSum=0.249;SOR=0.998	GT:AD:GQ:PGT:PID:PL	0/1:15,15:99:0|1:10433382_T_C:632,0,601
+20	10433391	.	T	C	623.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.300;AS_FS=0.000;AS_MQ=57.05;AS_MQRankSum=1.300;AS_RAW_BaseQRankSum=|-0.3,1;AS_RAW_MQ=51662.00|52082.00;AS_RAW_MQRankSum=|1.3,1;AS_RAW_ReadPosRankSum=|1.5,1;AS_ReadPosRankSum=1.500;AS_SB_TABLE=14,4|13,3;AS_SOR=0.859;BaseQRankSum=-2.840e-01;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.24;MQRankSum=1.33;QD=18.34;RAW_MQ=103744.00;ReadPosRankSum=1.54;SOR=0.859	GT:AD:GQ:PGT:PID:PL	0/1:18,16:99:0|1:10433382_T_C:631,0,673
+20	10433468	.	T	C	645.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=2.955;AS_MQ=58.84;AS_MQRankSum=0.000;AS_RAW_BaseQRankSum=|-1.4,1;AS_RAW_MQ=63049.00|69241.00;AS_RAW_MQRankSum=|0.0,1;AS_RAW_ReadPosRankSum=|1.4,1;AS_ReadPosRankSum=1.400;AS_SB_TABLE=13,5|12,8;AS_SOR=0.324;BaseQRankSum=-1.312e+00;DP=38;ExcessHet=3.0103;FS=2.955;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=0.076;QD=16.99;RAW_MQ=132290.00;ReadPosRankSum=1.46;SOR=0.324	GT:AD:GQ:PL	0/1:18,20:99:653,0,572
+20	10433560	.	C	A	987.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.400;AS_FS=5.027;AS_MQ=59.25;AS_MQRankSum=-1.100;AS_RAW_BaseQRankSum=|3.4,1;AS_RAW_MQ=111600.00|87769.00;AS_RAW_MQRankSum=|-1.1,1;AS_RAW_ReadPosRankSum=|1.3,1;AS_ReadPosRankSum=1.300;AS_SB_TABLE=30,1|22,3;AS_SOR=0.129;BaseQRankSum=3.50;DP=56;ExcessHet=3.0103;FS=5.027;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=-1.078e+00;QD=17.64;RAW_MQ=199369.00;ReadPosRankSum=1.38;SOR=0.129	GT:AD:GQ:PGT:PID:PL	0/1:31,25:99:0|1:10433560_C_A:995,0,3032
+20	10433575	.	C	T	1143.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.800;AS_FS=1.568;AS_MQ=57.81;AS_MQRankSum=-1.200;AS_RAW_BaseQRankSum=|3.8,1;AS_RAW_MQ=119641.00|100251.00;AS_RAW_MQRankSum=|-1.2,1;AS_RAW_ReadPosRankSum=|0.8,1;AS_ReadPosRankSum=0.800;AS_SB_TABLE=31,3|26,4;AS_SOR=0.375;BaseQRankSum=3.81;DP=64;ExcessHet=3.0103;FS=1.568;MLEAC=1;MLEAF=0.500;MQ=58.62;MQRankSum=-1.123e+00;QD=17.87;RAW_MQ=219892.00;ReadPosRankSum=0.830;SOR=0.375	GT:AD:GQ:PGT:PID:PL	0/1:34,30:99:0|1:10433560_C_A:1151,0,3385
+20	10433594	.	C	T	1105.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=4.800;AS_FS=1.535;AS_MQ=54.33;AS_MQRankSum=-2.400;AS_RAW_BaseQRankSum=|4.8,1;AS_RAW_MQ=108841.00|85615.00;AS_RAW_MQRankSum=|-2.4,1;AS_RAW_ReadPosRankSum=|-0.6,1;AS_ReadPosRankSum=-0.600;AS_SB_TABLE=28,3|25,4;AS_SOR=0.415;BaseQRankSum=4.82;DP=61;ExcessHet=3.0103;FS=1.535;MLEAC=1;MLEAF=0.500;MQ=56.66;MQRankSum=-2.334e+00;QD=18.43;RAW_MQ=195825.00;ReadPosRankSum=-5.020e-01;SOR=0.415	GT:AD:GQ:PGT:PID:PL	0/1:31,29:99:0|1:10433560_C_A:1113,0,3070
+20	10433809	.	A	G	1135.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.400;AS_FS=0.968;AS_MQ=60.00;AS_MQRankSum=0.000;AS_RAW_BaseQRankSum=|1.4,1;AS_RAW_MQ=115200.00|122400.00;AS_RAW_MQRankSum=|0.0,1;AS_RAW_ReadPosRankSum=|-0.5,1;AS_ReadPosRankSum=-0.500;AS_SB_TABLE=13,19|12,22;AS_SOR=0.930;BaseQRankSum=1.41;DP=68;ExcessHet=3.0103;FS=0.968;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=0.00;QD=17.21;RAW_MQ=242569.00;ReadPosRankSum=-4.450e-01;SOR=0.930	GT:AD:GQ:PL	0/1:32,34:99:1143,0,1041
+20	10433955	.	C	CGTGTGTGTGTAT	1027.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_MQ=40.57;AS_MQRankSum=-4.000;AS_RAW_BaseQRankSum=|0.4,1;AS_RAW_MQ=59810.00|39497.00;AS_RAW_MQRankSum=|-4.0,1;AS_RAW_ReadPosRankSum=|-0.8,1;AS_ReadPosRankSum=-0.800;AS_SB_TABLE=12,6|16,8;AS_SOR=0.710;BaseQRankSum=0.422;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.96;MQRankSum=-4.001e+00;QD=24.47;RAW_MQ=117307.00;ReadPosRankSum=-7.890e-01;SOR=0.710	GT:AD:GQ:PL	0/1:18,24:99:1035,0,1217
+20	10434177	.	A	T	1467.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.900;AS_FS=0.888;AS_MQ=55.78;AS_MQRankSum=-2.500;AS_RAW_BaseQRankSum=|0.9,1;AS_RAW_MQ=108000.00|133784.00;AS_RAW_MQRankSum=|-2.5,1;AS_RAW_ReadPosRankSum=|-0.9,1;AS_ReadPosRankSum=-0.900;AS_SB_TABLE=15,15|23,20;AS_SOR=0.836;BaseQRankSum=0.903;DP=74;ExcessHet=3.0103;FS=0.888;MLEAC=1;MLEAF=0.500;MQ=57.58;MQRankSum=-2.473e+00;QD=20.10;RAW_MQ=245384.00;ReadPosRankSum=-8.910e-01;SOR=0.836	GT:AD:GQ:PL	0/1:30,43:99:1475,0,936
+20	10434258	.	G	A	1235.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.000;AS_FS=0.000;AS_MQ=52.93;AS_MQRankSum=-2.900;AS_RAW_BaseQRankSum=|3.0,1;AS_RAW_MQ=109369.00|106451.00;AS_RAW_MQRankSum=|-2.9,1;AS_RAW_ReadPosRankSum=|-0.2,1;AS_ReadPosRankSum=-0.200;AS_SB_TABLE=19,12|24,14;AS_SOR=0.776;BaseQRankSum=3.06;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.99;MQRankSum=-2.871e+00;QD=17.91;RAW_MQ=219420.00;ReadPosRankSum=-1.550e-01;SOR=0.776	GT:AD:GQ:PL	0/1:31,38:99:1243,0,1003
+20	10434384	.	TA	T	782.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.100;AS_FS=0.000;AS_MQ=60.00;AS_MQRankSum=1.000;AS_RAW_BaseQRankSum=|-0.1,1;AS_RAW_MQ=123769.00|118800.00;AS_RAW_MQRankSum=|1.0,1;AS_RAW_ReadPosRankSum=|0.4,1;AS_ReadPosRankSum=0.400;AS_SB_TABLE=22,13|21,12;AS_SOR=0.723;BaseQRankSum=-1.000e-01;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=1.00;QD=11.51;RAW_MQ=253369.00;ReadPosRankSum=0.497;SOR=0.723	GT:AD:GQ:PL	0/1:35,33:99:790,0,846
+20	10434519	.	T	C	1464.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-3.200;AS_FS=1.877;AS_MQ=60.00;AS_MQRankSum=0.000;AS_RAW_BaseQRankSum=|-3.2,1;AS_RAW_MQ=126000.00|154800.00;AS_RAW_MQRankSum=|0.0,1;AS_RAW_ReadPosRankSum=|-0.8,1;AS_ReadPosRankSum=-0.800;AS_SB_TABLE=18,17|19,24;AS_SOR=0.900;BaseQRankSum=-3.137e+00;DP=78;ExcessHet=3.0103;FS=1.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.78;RAW_MQ=280800.00;ReadPosRankSum=-7.490e-01;SOR=0.900	GT:AD:GQ:PL	0/1:35,43:99:1472,0,1192
+20	10435067	.	GTA	G	1446.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.600;AS_FS=3.289;AS_MQ=60.00;AS_MQRankSum=0.000;AS_RAW_BaseQRankSum=|2.6,1;AS_RAW_MQ=108000.00|133200.00;AS_RAW_MQRankSum=|0.0,1;AS_RAW_ReadPosRankSum=|-0.2,1;AS_ReadPosRankSum=-0.200;AS_SB_TABLE=15,15|22,15;AS_SOR=1.121;BaseQRankSum=2.60;DP=67;ExcessHet=3.0103;FS=3.289;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.59;RAW_MQ=241200.00;ReadPosRankSum=-1.830e-01;SOR=1.121	GT:AD:GQ:PL	0/1:30,37:99:1454,0,1191
+20	10435948	.	A	C	1137.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-4.700;AS_FS=3.002;AS_MQ=54.65;AS_MQRankSum=-3.200;AS_RAW_BaseQRankSum=|-4.7,1;AS_RAW_MQ=144000.00|107528.00;AS_RAW_MQRankSum=|-3.2,1;AS_RAW_ReadPosRankSum=|-1.6,1;AS_ReadPosRankSum=-1.600;AS_SB_TABLE=19,21|20,16;AS_SOR=0.855;BaseQRankSum=-4.692e+00;DP=76;ExcessHet=3.0103;FS=3.002;MLEAC=1;MLEAF=0.500;MQ=57.53;MQRankSum=-3.121e+00;QD=14.97;RAW_MQ=251528.00;ReadPosRankSum=-1.594e+00;SOR=0.855	GT:AD:GQ:PL	0/1:40,36:99:1145,0,1413
+20	10436227	.	TTTTATTTATTTATTTATTTA	T,TTTTATTTATTTATTTATTTATTTA	1208.06	.	AC=1,1;AF=0.500,0.500;AN=2;AS_BaseQRankSum=nul,nul;AS_FS=0.000,0.000;AS_MQ=32.72,53.03;AS_MQRankSum=nul,nul;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=3600.00|25702.00|19682.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_ReadPosRankSum=nul,nul;AS_SB_TABLE=1,0|14,10|4,3;AS_SOR=0.382,0.330;BaseQRankSum=-1.450e+00;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.77;MQRankSum=-1.660e+00;QD=28.73;RAW_MQ=201025.00;ReadPosRankSum=1.30;SOR=0.379	GT:AD:GQ:PL	1/2:1,24,7:99:1225,241,589,947,0,970
+20	10436415	.	A	G	1190.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.800;AS_FS=9.312;AS_MQ=59.42;AS_MQRankSum=0.400;AS_RAW_BaseQRankSum=|-2.8,1;AS_RAW_MQ=81904.00|141241.00;AS_RAW_MQRankSum=|0.4,1;AS_RAW_ReadPosRankSum=|-0.1,1;AS_ReadPosRankSum=-0.100;AS_SB_TABLE=15,8|17,23;AS_SOR=0.739;BaseQRankSum=-2.775e+00;DP=63;ExcessHet=3.0103;FS=9.312;MLEAC=1;MLEAF=0.500;MQ=59.51;MQRankSum=0.399;QD=18.90;RAW_MQ=223145.00;ReadPosRankSum=-6.300e-02;SOR=0.739	GT:AD:GQ:PL	0/1:23,40:99:1198,0,691
+20	10436582	.	A	G	1187.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=3.189;AS_MQ=52.86;AS_MQRankSum=-2.700;AS_RAW_BaseQRankSum=|-1.4,1;AS_RAW_MQ=117410.00|103379.00;AS_RAW_MQRankSum=|-2.7,1;AS_RAW_ReadPosRankSum=|0.2,1;AS_ReadPosRankSum=0.200;AS_SB_TABLE=16,18|21,16;AS_SOR=0.906;BaseQRankSum=-1.326e+00;DP=71;ExcessHet=3.0103;FS=3.189;MLEAC=1;MLEAF=0.500;MQ=55.76;MQRankSum=-2.639e+00;QD=16.73;RAW_MQ=220789.00;ReadPosRankSum=0.267;SOR=0.906	GT:AD:GQ:PL	0/1:34,37:99:1195,0,1113
+20	10436700	.	A	G	1333.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=2.012;AS_MQ=59.53;AS_MQRankSum=-0.900;AS_RAW_BaseQRankSum=|-1.4,1;AS_RAW_MQ=108000.00|141769.00;AS_RAW_MQRankSum=|-0.9,1;AS_RAW_ReadPosRankSum=|0.5,1;AS_ReadPosRankSum=0.500;AS_SB_TABLE=18,12|21,19;AS_SOR=0.449;BaseQRankSum=-1.329e+00;DP=70;ExcessHet=3.0103;FS=2.012;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-8.370e-01;QD=19.05;RAW_MQ=249769.00;ReadPosRankSum=0.581;SOR=0.449	GT:AD:GQ:PL	0/1:30,40:99:1341,0,961
+20	10436908	.	C	G	1361.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.900;AS_FS=4.557;AS_MQ=58.89;AS_MQRankSum=-1.000;AS_RAW_BaseQRankSum=|-0.9,1;AS_RAW_MQ=145849.00|145638.00;AS_RAW_MQRankSum=|-1.0,1;AS_RAW_ReadPosRankSum=|-0.2,1;AS_ReadPosRankSum=-0.200;AS_SB_TABLE=15,26|11,31;AS_SOR=1.252;BaseQRankSum=-8.440e-01;DP=83;ExcessHet=3.0103;FS=4.557;MLEAC=1;MLEAF=0.500;MQ=59.26;MQRankSum=-9.940e-01;QD=16.40;RAW_MQ=291487.00;ReadPosRankSum=-1.480e-01;SOR=1.252	GT:AD:GQ:PL	0/1:41,42:99:1369,0,1378
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/hailOutput.chr20snippet.sites_only.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/hailOutput.chr20snippet.sites_only.vcf.idx
new file mode 100644
index 0000000000000000000000000000000000000000..99bdfa50a448374764ab704c0474124f51c2a156
GIT binary patch
literal 154586
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