VS-1336 - It's not a site FILTER

.dockstore.yml

@@ -288,6 +288,7 @@ workflows:
          branches:
              - master
              - ah_var_store
+             - gg_VS-1336_ItsNotASiteFilter
          tags:
              - /.*/
    - name: GvsQuickstartHailIntegration
@@ -297,6 +298,7 @@ workflows:
          branches:
              - master
              - ah_var_store
+             - gg_VS-1336_ItsNotASiteFilter
          tags:
              - /.*/
    - name: GvsQuickstartIntegration
@@ -306,6 +308,7 @@ workflows:
          branches:
              - master
              - ah_var_store
+             - gg_VS-1336_ItsNotASiteFilter
              - vs_1334_vcf_max_alt_alleles
          tags:
              - /.*/

scripts/variantstore/wdl/GvsQuickstartIntegration.wdl

@@ -34,7 +34,7 @@ workflow GvsQuickstartIntegration {
     File full_wgs_interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
     File full_exome_interval_list = "gs://gcp-public-data--broad-references/hg38/v0/bge_exome_calling_regions.v1.1.interval_list"
     String expected_subdir = if (!chr20_X_Y_only) then "all_chrs/"  else ""
-    File expected_output_prefix = "gs://gvs-internal-quickstart/integration/2024-03-13/" + expected_subdir
+    File expected_output_prefix = "gs://gvs-internal-quickstart/integration/2024-05-13/" + expected_subdir
 
     # WDL 1.0 trick to set a variable ('none') to be undefined.
     if (false) {

scripts/variantstore/wdl/GvsUtils.wdl

@@ -74,7 +74,7 @@ task GetToolVersions {
     String cloud_sdk_slim_docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:435.0.0-slim"
     String variants_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/variants:2024-04-22-alpine-32804b134a75"
     String variants_nirvana_docker = "us.gcr.io/broad-dsde-methods/variantstore:nirvana_2022_10_19"
-    String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024-05-01-gatkbase-617d4d1c7f64"
+    String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2024_05_10-gatkbase-9bd39afc04ae"
     String real_time_genomics_docker = "docker.io/realtimegenomics/rtg-tools:latest"
     String gotc_imputation_docker = "us.gcr.io/broad-gotc-prod/imputation-bcf-vcf:1.0.5-1.10.2-0.1.16-1649948623"
     String plink_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/plink2:2024-04-23-slim-a0a65f52cc0e"

src/main/java/org/broadinstitute/hellbender/tools/gvs/common/FilterSensitivityTools.java

@@ -123,11 +123,20 @@
                 "Site failed " + model + " model VQSLOD cutoff of " + vqsLodThreshold.toString());
     }
 
-    public static VCFHeaderLine getTruthSensitivityHeader(Double truthSensitivityThreshold, Double vqsLodThreshold, String model) {
+    public static VCFHeaderLine getTruthSensitivityFilterHeader(Double truthSensitivityThreshold, Double vqsLodThreshold, String model) {
         if (truthSensitivityThreshold == null) {  // at this point, we know that all vqsr threshold inputs are null, so use defaults
             truthSensitivityThreshold = GATKVCFConstants.SNP.contains(model) ? DEFAULT_TRUTH_SENSITIVITY_THRESHOLD_SNPS : DEFAULT_TRUTH_SENSITIVITY_THRESHOLD_INDELS;
         }
         return new VCFFilterHeaderLine(GATKVCFConstants.VQSR_FAILURE_PREFIX + model,
                 "Site failed " + model + " model sensitivity cutoff (" + truthSensitivityThreshold + "), corresponding with VQSLOD cutoff of " + vqsLodThreshold.toString());
     }
+
+    public static VCFHeaderLine getTruthSensitivityHeader(Double truthSensitivityThreshold, Double vqsLodThreshold, String model) {
+        if (truthSensitivityThreshold == null) {  // at this point, we know that all vqsr threshold inputs are null, so use defaults
+            truthSensitivityThreshold = GATKVCFConstants.SNP.contains(model) ? DEFAULT_TRUTH_SENSITIVITY_THRESHOLD_SNPS : DEFAULT_TRUTH_SENSITIVITY_THRESHOLD_INDELS;
+        }
+        return new VCFHeaderLine(GATKVCFConstants.VQSR_FAILURE_PREFIX + model,
+                "Sample Genotype FT filter value indicating that the genotyped allele failed " + model + " model sensitivity cutoff (" + truthSensitivityThreshold + "), corresponding with VQSLOD cutoff of " + vqsLodThreshold.toString());
+    }
+
 }

src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohort.java

@@ -130,7 +130,7 @@
 
     @Argument(
             fullName = "vqs-score-filter-by-site",
-            doc = "If Variant Quality Score filtering is applied, it should be at a site level. Default is false",
+            doc = "If Variant Quality Score filtering (either VETS or VQSR) is applied, it should be at a site level. Default is false",
             optional = true
     )
     // historical note that this parameter was previously named 'vqsr-score-filter-by-site', changed as it's not VQSR-specific
@@ -340,8 +340,15 @@
                     vqsLodSNPThreshold = FilterSensitivityTools.getVqslodThreshold(trancheMaps.get(GATKVCFConstants.SNP), truthSensitivitySNPThreshold, GATKVCFConstants.SNP);
                     vqsLodINDELThreshold = FilterSensitivityTools.getVqslodThreshold(trancheMaps.get(GATKVCFConstants.INDEL), truthSensitivityINDELThreshold, GATKVCFConstants.INDEL);
                     // set headers
-                    extraHeaderLines.add(FilterSensitivityTools.getTruthSensitivityHeader(truthSensitivitySNPThreshold, vqsLodSNPThreshold, GATKVCFConstants.SNP));
-                    extraHeaderLines.add(FilterSensitivityTools.getTruthSensitivityHeader(truthSensitivityINDELThreshold, vqsLodINDELThreshold, GATKVCFConstants.INDEL));
+
+                    if (vqScoreFilteringType.equals(VQScoreFilteringType.SITES)) {
+                        extraHeaderLines.add(FilterSensitivityTools.getTruthSensitivityFilterHeader(truthSensitivitySNPThreshold, vqsLodSNPThreshold, GATKVCFConstants.SNP));
+                        extraHeaderLines.add(FilterSensitivityTools.getTruthSensitivityFilterHeader(truthSensitivityINDELThreshold, vqsLodINDELThreshold, GATKVCFConstants.INDEL));
+                    }
+                    else if (vqScoreFilteringType.equals(VQScoreFilteringType.GENOTYPE)) {
+                        extraHeaderLines.add(FilterSensitivityTools.getTruthSensitivityHeader(truthSensitivitySNPThreshold, vqsLodSNPThreshold, GATKVCFConstants.SNP));
+                        extraHeaderLines.add(FilterSensitivityTools.getTruthSensitivityHeader(truthSensitivityINDELThreshold, vqsLodINDELThreshold, GATKVCFConstants.INDEL));
+                    }
                 }
             } else {
                 extraHeaderLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.SCORE_KEY));
@@ -358,15 +365,23 @@
                 truthSensitivityINDELThreshold /= 100.0;
                 logger.info("Passing all INDEL variants with " + GATKVCFConstants.CALIBRATION_SENSITIVITY_KEY + " < " + truthSensitivityINDELThreshold);
 
-                extraHeaderLines.add(new VCFFilterHeaderLine(GATKVCFConstants.CALIBRATION_SENSITIVITY_FAILURE_SNP,
-                        "Site failed SNP model calibration sensitivity cutoff (" + truthSensitivitySNPThreshold.toString() + ")"));
-                extraHeaderLines.add(new VCFFilterHeaderLine(GATKVCFConstants.CALIBRATION_SENSITIVITY_FAILURE_INDEL,
-                        "Site failed INDEL model calibration sensitivity cutoff (" + truthSensitivityINDELThreshold.toString() + ")"));
+                if (vqScoreFilteringType.equals(VQScoreFilteringType.SITES)) {
+                    extraHeaderLines.add(new VCFFilterHeaderLine(GATKVCFConstants.CALIBRATION_SENSITIVITY_FAILURE_SNP,
+                            "Site failed SNP model calibration sensitivity cutoff (" + truthSensitivitySNPThreshold.toString() + ")"));
+                    extraHeaderLines.add(new VCFFilterHeaderLine(GATKVCFConstants.CALIBRATION_SENSITIVITY_FAILURE_INDEL,
+                            "Site failed INDEL model calibration sensitivity cutoff (" + truthSensitivityINDELThreshold.toString() + ")"));
+                }
+                else if (vqScoreFilteringType.equals(VQScoreFilteringType.GENOTYPE)) {
+                    extraHeaderLines.add(new VCFHeaderLine(GATKVCFConstants.CALIBRATION_SENSITIVITY_FAILURE_SNP,
+                            "Sample Genotype FT filter value indicating that the genotyped allele failed SNP model calibration sensitivity cutoff (" + truthSensitivitySNPThreshold.toString() + ")"));
+                    extraHeaderLines.add(new VCFHeaderLine(GATKVCFConstants.CALIBRATION_SENSITIVITY_FAILURE_INDEL,
+                            "Sample Genotype FT filter value indicating that the genotyped allele failed INDEL model calibration sensitivity cutoff (" + truthSensitivityINDELThreshold.toString() + ")"));
+                }
             }
         }
 
         if (vqScoreFilteringType.equals(VQScoreFilteringType.GENOTYPE)) {
-            extraHeaderLines.add(new VCFFormatHeaderLine("FT", 1, VCFHeaderLineType.String, "Genotype Filter Field"));
+            extraHeaderLines.add(new VCFFormatHeaderLine("FT", 1, VCFHeaderLineType.String, "Sample Genotype Filter Field"));
         }
 
         if (emitPLs) {

src/test/java/org/broadinstitute/hellbender/tools/gvs/common/FilterSensitivityToolsTest.java

@@ -15,12 +15,12 @@
 public class FilterSensitivityToolsTest {
 
     // for testing inputs
-    private Double definedDoubleInput = 0.0;
-    private Double undefinedDoubleInput = null;
-    private String definedStringInput = "I'm defined!";
-    private String undefinedStringInput = null;
+    private final Double definedDoubleInput = 0.0;
+    private final Double undefinedDoubleInput = null;
+    private final String definedStringInput = "I'm defined!";
+    private final String undefinedStringInput = null;
 
-    private Map<Double, Double> testTrancheMap = new TreeMap<>();
+    private final Map<Double, Double> testTrancheMap = new TreeMap<>();
 
     @BeforeMethod
     public void setUp() {
@@ -211,7 +211,7 @@ public void testGetTruthSensitivityHeaderSNP() {
         VCFFilterHeaderLine expectedHeader = new VCFFilterHeaderLine(GATKVCFConstants.VQSR_FAILURE_PREFIX + model,
                 "Site failed SNP model sensitivity cutoff (90.0), corresponding with VQSLOD cutoff of 0.0");
 
-        assertEquals(getTruthSensitivityHeader(truthSensitivityThreshold, vqsLodThreshold, GATKVCFConstants.SNP), expectedHeader);
+        assertEquals(getTruthSensitivityFilterHeader(truthSensitivityThreshold, vqsLodThreshold, GATKVCFConstants.SNP), expectedHeader);
     }
 
     @Test
@@ -222,7 +222,7 @@ public void testGetTruthSensitivityHeaderINDEL() {
         VCFFilterHeaderLine expectedHeader = new VCFFilterHeaderLine(GATKVCFConstants.VQSR_FAILURE_PREFIX + model,
                 "Site failed INDEL model sensitivity cutoff (90.0), corresponding with VQSLOD cutoff of 0.0");
 
-        assertEquals(getTruthSensitivityHeader(truthSensitivityThreshold, vqsLodThreshold, GATKVCFConstants.INDEL), expectedHeader);
+        assertEquals(getTruthSensitivityFilterHeader(truthSensitivityThreshold, vqsLodThreshold, GATKVCFConstants.INDEL), expectedHeader);
     }
 
 }