Recognize MEI DELs with ALT format <DEL:ME> in SVAnnotate (#8125)

broadinstitute · Jan 3, 2023 · 3687415 · 3687415
1 parent 0261d43
commit 3687415
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Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotateEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotateEngine.java
@@ -14,6 +14,7 @@
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature;
 import org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature;
+import org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils;
 
 import java.util.*;
 
@@ -476,13 +477,8 @@ protected static StructuralVariantAnnotationType getSVType(final VariantContext
             }
             return StructuralVariantAnnotationType.BND;
         } else if (alt.isSymbolic()) {
-            if (alt.toString().contains("INS")) {
-                // account for <INS:ME>, etc. types
-                return StructuralVariantAnnotationType.INS;
-            } else {
-                // parse ALT as symbolic allele, assuming format <SVTYPE>
-                return StructuralVariantAnnotationType.valueOf(alt.toString().substring(1, alt.toString().length()-1));
-            }
+            // parse ALT as symbolic allele, assuming format <SVTYPE> or <SVTYPE:SUBTYPE_1:...:SUBTYPE_N>
+            return StructuralVariantAnnotationType.valueOf(GATKSVVariantContextUtils.getSymbolicAlleleSymbols(alt)[0]);
         } else {
             throw new IllegalArgumentException("Unexpected ALT allele: " + alt +
                     ". Expected breakpoint or symbolic ALT allele representing a structural variant record.");

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotateEngineUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotateEngineUnitTest.java
@@ -425,6 +425,12 @@ public Object[][] getSVTypesAndSegmentsTestData() {
                         createListOfSVSegments(SVAnnotateEngine.StructuralVariantAnnotationType.DEL,
                                 new SimpleInterval[]{ new SimpleInterval("chr22", 10510000, 10694100)}),
                         null},
+                { createVariantContext("chr22", 10510000, 10694100, "chr22", null, "N",
+                        "<DEL:ME:LINE1>", 184100, null, null, null),
+                        SVAnnotateEngine.StructuralVariantAnnotationType.DEL,
+                        createListOfSVSegments(SVAnnotateEngine.StructuralVariantAnnotationType.DEL,
+                                new SimpleInterval[]{ new SimpleInterval("chr22", 10510000, 10694100)}),
+                        null},
                 { createVariantContext("chr22", 10524000, 10710000, "chr22", null, "N",
                         "<DUP>", 186000, null, null, null),
                         SVAnnotateEngine.StructuralVariantAnnotationType.DUP,