Remove SPLICE_AI as a default score

exomiser · Feb 27, 2024 · 7471065 · 7471065
1 parent 14091ac
commit 7471065
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Showing 13 changed files with 15 additions and 15 deletions.
diff --git a/exomiser-cli/src/main/resources/examples/preset-exome-analysis.yml b/exomiser-cli/src/main/resources/examples/preset-exome-analysis.yml
@@ -37,7 +37,7 @@ frequencySources: [
 # REMM is trained on non-coding regulatory regions
 # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files
 # and updated their location in the application.properties. Exomiser will not run without this.
-pathogenicitySources: [ REVEL, MVP, SPLICE_AI ]
+pathogenicitySources: [ REVEL, MVP ]
 #this is the standard exomiser order.
 steps: [
     failedVariantFilter: { },

diff --git a/exomiser-cli/src/main/resources/examples/preset-genome-analysis.yml b/exomiser-cli/src/main/resources/examples/preset-genome-analysis.yml
@@ -37,7 +37,7 @@ frequencySources: [
 # REMM is trained on non-coding regulatory regions
 # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files
 # and updated their location in the application.properties. Exomiser will not run without this.
-pathogenicitySources: [ REVEL, MVP, REMM, SPLICE_AI ]
+pathogenicitySources: [ REVEL, MVP, REMM ]
 # this is the recommended order for a genome-sized analysis.
 steps: [
     hiPhivePrioritiser: { },

diff --git a/exomiser-cli/src/main/resources/examples/test-analysis-exome.yml b/exomiser-cli/src/main/resources/examples/test-analysis-exome.yml
@@ -55,7 +55,7 @@ analysis:
   # REMM is trained on non-coding regulatory regions
   # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files
   # and updated their location in the application.properties. Exomiser will not run without this.
-    pathogenicitySources: [ REVEL, MVP, SPLICE_AI ]
+    pathogenicitySources: [ REVEL, MVP ]
   # this is the standard exomiser order.
   # all steps are optional
     steps: [

diff --git a/exomiser-cli/src/main/resources/examples/test-analysis-genome.yml b/exomiser-cli/src/main/resources/examples/test-analysis-genome.yml
@@ -55,7 +55,7 @@ analysis:
   # REMM is trained on non-coding regulatory regions
   # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files
   # and updated their location in the application.properties. Exomiser will not run without this.
-    pathogenicitySources: [ REVEL, MVP, REMM, SPLICE_AI ]
+    pathogenicitySources: [ REVEL, MVP, REMM ]
   # this is the recommended order for a genome-sized analysis.
   # all steps are optional
     steps: [

diff --git a/exomiser-cli/src/main/resources/examples/test-analysis-multisample.yml b/exomiser-cli/src/main/resources/examples/test-analysis-multisample.yml
@@ -54,7 +54,7 @@ analysis:
   # REMM is trained on non-coding regulatory regions
   # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files
   # and updated their location in the application.properties. Exomiser will not run without this.
-    pathogenicitySources: [ REVEL, MVP, SPLICE_AI ]
+    pathogenicitySources: [ REVEL, MVP ]
   # this is the standard exomiser order.
   # all steps are optional
     steps: [

diff --git a/exomiser-cli/src/test/java/org/monarchinitiative/exomiser/cli/CommandLineJobReaderTest.java b/exomiser-cli/src/test/java/org/monarchinitiative/exomiser/cli/CommandLineJobReaderTest.java
@@ -264,7 +264,7 @@ class CommandLineJobReaderTest {
 //                    FrequencySource.GNOMAD_G_OTH,
                     FrequencySource.GNOMAD_G_SAS
             ))
-            .pathogenicitySources(ImmutableSet.of(REVEL, MVP, SPLICE_AI))
+            .pathogenicitySources(ImmutableSet.of(REVEL, MVP))
             .addFailedVariantFilter()
             .addVariantEffectFilter(ImmutableSet.of(
                     FIVE_PRIME_UTR_EXON_VARIANT,

diff --git a/exomiser-cli/src/test/resources/exome-analysis.yml b/exomiser-cli/src/test/resources/exome-analysis.yml
@@ -42,7 +42,7 @@ frequencySources: [
 # REMM is trained on non-coding regulatory regions
 # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files
 # and updated their location in the application.properties. Exomiser will not run without this.
-pathogenicitySources: [ REVEL, MVP, SPLICE_AI ]
+pathogenicitySources: [ REVEL, MVP ]
 #this is the standard exomiser order.
 #all steps are optional
 steps: [

diff --git a/exomiser-cli/src/test/resources/pfeiffer-analysis-v8-12.yml b/exomiser-cli/src/test/resources/pfeiffer-analysis-v8-12.yml
@@ -54,7 +54,7 @@ analysis:
   # REMM is trained on non-coding regulatory regions
   # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files
   # and updated their location in the application.properties. Exomiser will not run without this.
-  pathogenicitySources: [ REVEL, MVP, SPLICE_AI ]
+  pathogenicitySources: [ REVEL, MVP ]
   #this is the standard exomiser order.
   #all steps are optional
   steps: [

diff --git a/exomiser-cli/src/test/resources/pfeiffer-job-phenopacket.yml b/exomiser-cli/src/test/resources/pfeiffer-job-phenopacket.yml
@@ -93,7 +93,7 @@ analysis:
   # REMM is trained on non-coding regulatory regions
   # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files
   # and updated their location in the application.properties. Exomiser will not run without this.
-  pathogenicitySources: [ REVEL, MVP, SPLICE_AI ]
+  pathogenicitySources: [ REVEL, MVP ]
   #this is the standard exomiser order.
   #all steps are optional
   steps: [

diff --git a/exomiser-cli/src/test/resources/pfeiffer-job-sample.yml b/exomiser-cli/src/test/resources/pfeiffer-job-sample.yml
@@ -61,7 +61,7 @@ analysis:
   # REMM is trained on non-coding regulatory regions
   # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files
   # and updated their location in the application.properties. Exomiser will not run without this.
-  pathogenicitySources: [ REVEL, MVP, SPLICE_AI ]
+  pathogenicitySources: [ REVEL, MVP ]
   #this is the standard exomiser order.
   #all steps are optional
   steps: [

diff --git a/exomiser-cli/src/test/resources/test-analysis-exome.yml b/exomiser-cli/src/test/resources/test-analysis-exome.yml
@@ -55,7 +55,7 @@ analysis:
   # REMM is trained on non-coding regulatory regions
   # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files
   # and updated their location in the application.properties. Exomiser will not run without this.
-  pathogenicitySources: [ REVEL, MVP, SPLICE_AI ]
+  pathogenicitySources: [ REVEL, MVP ]
   # this is the standard exomiser order.
   # all steps are optional
   steps: [

diff --git a/...ore/src/main/java/org/monarchinitiative/exomiser/core/analysis/AnalysisPresetBuilder.java b/...ore/src/main/java/org/monarchinitiative/exomiser/core/analysis/AnalysisPresetBuilder.java
@@ -115,7 +115,7 @@ protected Analysis buildGenomePreset() {
                 .analysisMode(AnalysisMode.PASS_ONLY)
                 .inheritanceModes(DEFAULT_INHERITANCE_MODE_OPTIONS)
                 .frequencySources(DEFAULT_FREQUENCY_SOURCES)
-                .pathogenicitySources(EnumSet.of(REVEL, MVP, REMM, SPLICE_AI))
+                .pathogenicitySources(EnumSet.of(REVEL, MVP, REMM))
                 .addHiPhivePrioritiser(HI_PHIVE_OPTIONS)
                 .addPriorityScoreFilter(PriorityType.HIPHIVE_PRIORITY, 0.5f)// will remove a lot of the weak PPI hits
                 .addFailedVariantFilter()
@@ -132,7 +132,7 @@ protected Analysis buildExomePreset() {
                 .analysisMode(AnalysisMode.PASS_ONLY)
                 .inheritanceModes(DEFAULT_INHERITANCE_MODE_OPTIONS)
                 .frequencySources(DEFAULT_FREQUENCY_SOURCES)
-                .pathogenicitySources(EnumSet.of(REVEL, MVP, SPLICE_AI))
+                .pathogenicitySources(EnumSet.of(REVEL, MVP))
                 .addVariantEffectFilter(EnumSet.of(
                         VariantEffect.FIVE_PRIME_UTR_EXON_VARIANT,
                         VariantEffect.FIVE_PRIME_UTR_INTRON_VARIANT,

diff --git a/...src/test/java/org/monarchinitiative/exomiser/core/analysis/AnalysisPresetBuilderTest.java b/...src/test/java/org/monarchinitiative/exomiser/core/analysis/AnalysisPresetBuilderTest.java
@@ -53,7 +53,7 @@ public void testBuildExomePreset() {
         assertThat(analysis.getAnalysisMode(), equalTo(AnalysisMode.PASS_ONLY));
         assertThat(analysis.getInheritanceModeOptions(), equalTo(InheritanceModeOptions.defaults()));
         assertThat(analysis.getFrequencySources(), equalTo(FREQUENCY_SOURCES));
-        assertThat(analysis.getPathogenicitySources(), equalTo(Set.of(REVEL, MVP, SPLICE_AI)));
+        assertThat(analysis.getPathogenicitySources(), equalTo(Set.of(REVEL, MVP)));
         assertThat(analysis.getAnalysisSteps().stream().map(AnalysisStep::getClass).collect(Collectors.toList()),
                 equalTo(List.of(
                         VariantEffectFilter.class,
@@ -72,7 +72,7 @@ public void testBuildGenomePreset() {
         assertThat(analysis.getAnalysisMode(), equalTo(AnalysisMode.PASS_ONLY));
         assertThat(analysis.getInheritanceModeOptions(), equalTo(InheritanceModeOptions.defaults()));
         assertThat(analysis.getFrequencySources(), equalTo(FREQUENCY_SOURCES));
-        assertThat(analysis.getPathogenicitySources(), equalTo(Set.of(REVEL, MVP, REMM, SPLICE_AI)));
+        assertThat(analysis.getPathogenicitySources(), equalTo(Set.of(REVEL, MVP, REMM)));
         assertThat(analysis.getAnalysisSteps().stream().map(AnalysisStep::getClass).collect(Collectors.toList()),
                 equalTo(List.of(
                         HiPhivePriority.class,