diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/VepHelper.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/VepHelper.java index f191bef..7fca874 100644 --- 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 index 6f355b5..88f9c52 100644 --- 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 index eaa282e..960252a 100644 --- 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 index b085d05..302a6a0 100644 --- 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