Add pick to empty CSQ if no CSQ is present in the input

molgenis · Dec 17, 2024 · 8ece202 · 8ece202
1 parent bfab8d1
commit 8ece202
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Showing 4 changed files with 14 additions and 8 deletions.
diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/VepHelper.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/VepHelper.java
@@ -2,6 +2,7 @@
 
 import static java.util.Collections.singletonList;
 import static org.molgenis.vcf.decisiontree.runner.info.VepMetadataMapperImpl.ALLELE_NUM;
+import static org.molgenis.vcf.decisiontree.runner.info.VepMetadataMapperImpl.PICK;
 
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
@@ -52,6 +53,10 @@ public VcfRecord createEmptyCsqRecord(VcfRecord vcfRecord,
       values.add("");
     }
     values.set(fields.get(ALLELE_NUM).getIndex(), alleleIndex.toString());
+    NestedField pick = fields.get(PICK);
+    if(pick != null) {
+      values.set(pick.getIndex(), "1");
+    }
     VariantContext variantContext = vcfRecord.getVariantContext();
     VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variantContext);
     variantContextBuilder.attribute(nestedHeaderLine.getParentField().getId(),

diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/info/VepMetadataMapperImpl.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/info/VepMetadataMapperImpl.java
@@ -20,6 +20,7 @@
 public class VepMetadataMapperImpl implements VepMetadataMapper {
 
   public static final String ALLELE_NUM = "ALLELE_NUM";
+  public static final String PICK = "PICK";
   private static final String INFO_DESCRIPTION_PREFIX = "Consequence annotations from Ensembl VEP. Format: ";
 
   private final FieldMetadataService fieldMetadataService;

diff --git a/src/test/resources/example-classified.vcf b/src/test/resources/example-classified.vcf
@@ -45,7 +45,7 @@
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
 1	10042538	.	C	T	.	PASS	CSQ=LP|T|missense_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000377205|protein_coding|5/5||||763|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|HGNC|17877|1|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LP,|T|NMD_transcript_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000462686|nonsense_mediated_decay|5/6||||762|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1|||HGNC|17877|1|0.0001|0|0.0001|0|0|0|0.0001|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0.43|0|0.41|LP
 1	10042539	.	C	A,T	.	PASS	CSQ=LP|A|missense_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000377205|protein_coding|5/5||||763|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|HGNC|17877|1|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LP,LB|T|missense_variant&NMD_transcript_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000462686|nonsense_mediated_decay|5/6||||762|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|2||2|||HGNC|17877|2|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LB
-1	10042540	.	C	G	.	PASS	CLINVAR=LP;CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LP
-1	10042541	.	C	G	.	PASS	CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LB
-1	10042542	.	C	G	.	.	CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LB
-1	10042543	.	C	G	.	PASS	CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LP;FLAG1
+1	10042540	.	C	G	.	PASS	CLINVAR=LP;CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LP
+1	10042541	.	C	G	.	PASS	CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LB
+1	10042542	.	C	G	.	.	CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LB
+1	10042543	.	C	G	.	PASS	CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LP;FLAG1
diff --git a/src/test/resources/example-classified_paths-labels.vcf b/src/test/resources/example-classified_paths-labels.vcf
@@ -47,7 +47,7 @@
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
 1	10042538	.	C	T	.	PASS	CSQ=LP|T|missense_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000377205|protein_coding|5/5||||763|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|HGNC|17877|1|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LP|filter&vkgl&exit_lp|,|T|NMD_transcript_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000462686|nonsense_mediated_decay|5/6||||762|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1|||HGNC|17877|1|0.0001|0|0.0001|0|0|0|0.0001|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0.43|0|0.41|LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&exit_lp|
 1	10042539	.	C	A,T	.	PASS	CSQ=LP|A|missense_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000377205|protein_coding|5/5||||763|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|HGNC|17877|1|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LP|filter&vkgl&exit_lp|,LB|T|missense_variant&NMD_transcript_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000462686|nonsense_mediated_decay|5/6||||762|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|2||2|||HGNC|17877|2|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LB|filter&vkgl&exit_lb|
-1	10042540	.	C	G	.	PASS	CLINVAR=LP;CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LP|filter&vkgl&clinVar&exit_lp|
-1	10042541	.	C	G	.	PASS	CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LB|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lb|
-1	10042542	.	C	G	.	.	CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LB|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lb|
-1	10042543	.	C	G	.	PASS	CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lp|;FLAG1
+1	10042540	.	C	G	.	PASS	CLINVAR=LP;CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LP|filter&vkgl&clinVar&exit_lp|
+1	10042541	.	C	G	.	PASS	CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LB|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lb|
+1	10042542	.	C	G	.	.	CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LB|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lb|
+1	10042543	.	C	G	.	PASS	CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lp|;FLAG1