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

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merged 2 commits into from
Jan 3, 2023
Merged

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

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32514bb
recognize MEI DELs with ALT <DEL:ME> or similar
epiercehoffman Dec 8, 2022
3eb4c98
use utility method to get symbolic allele symbols
epiercehoffman Dec 8, 2022
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10 changes: 3 additions & 7 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotateEngine.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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.*;

Expand Down Expand Up @@ -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.");
Expand Down
6 changes: 6 additions & 0 deletions src/test/java/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotateEngineUnitTest.java
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Expand Up @@ -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,
Expand Down