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Improved descriptions for the SnpEff annotations in the VCF header 

(based on Eric's feedback).
This commit is contained in:
David Roazen 2011-08-17 14:55:32 -04:00
parent 784fb148b9
commit 53006da9a5
2 changed files with 14 additions and 14 deletions
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26
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
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@ -161,19 +161,19 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
public List<VCFInfoHeaderLine> getDescriptions() {
return Arrays.asList(
new VCFInfoHeaderLine(GENE_ID_KEY, 1, VCFHeaderLineType.String, "Gene ID"),
new VCFInfoHeaderLine(GENE_NAME_KEY, 1, VCFHeaderLineType.String, "Gene name"),
new VCFInfoHeaderLine(TRANSCRIPT_ID_KEY, 1, VCFHeaderLineType.String, "Transcript ID"),
new VCFInfoHeaderLine(EXON_ID_KEY, 1, VCFHeaderLineType.String, "Exon ID"),
new VCFInfoHeaderLine(EXON_RANK_KEY, 1, VCFHeaderLineType.Integer, "Exon rank"),
new VCFInfoHeaderLine(WITHIN_NON_CODING_GENE_KEY, 0, VCFHeaderLineType.Flag, "If present, gene is non-coding"),
new VCFInfoHeaderLine(EFFECT_KEY, 1, VCFHeaderLineType.String, "One of the most high-impact effects across all transcripts at this site"),
new VCFInfoHeaderLine(EFFECT_IMPACT_KEY, 1, VCFHeaderLineType.String, "Impact of the effect " + Arrays.toString(SnpEffConstants.EffectImpact.values())),
new VCFInfoHeaderLine(EFFECT_EXTRA_INFORMATION_KEY, 1, VCFHeaderLineType.String, "Additional information about the effect"),
new VCFInfoHeaderLine(OLD_NEW_AA_KEY, 1, VCFHeaderLineType.String, "Old/New amino acid"),
new VCFInfoHeaderLine(OLD_NEW_CODON_KEY, 1, VCFHeaderLineType.String, "Old/New codon"),
new VCFInfoHeaderLine(CODON_NUM_KEY, 1, VCFHeaderLineType.Integer, "Codon number"),
new VCFInfoHeaderLine(CDS_SIZE_KEY, 1, VCFHeaderLineType.Integer, "CDS size")
new VCFInfoHeaderLine(GENE_ID_KEY, 1, VCFHeaderLineType.String, "Gene ID for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(GENE_NAME_KEY, 1, VCFHeaderLineType.String, "Gene name for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(TRANSCRIPT_ID_KEY, 1, VCFHeaderLineType.String, "Transcript ID for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(EXON_ID_KEY, 1, VCFHeaderLineType.String, "Exon ID for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(EXON_RANK_KEY, 1, VCFHeaderLineType.Integer, "Exon rank for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(WITHIN_NON_CODING_GENE_KEY, 0, VCFHeaderLineType.Flag, "If this flag is present, the highest-impact effect resulting from the current variant is within a non-coding gene"),
new VCFInfoHeaderLine(EFFECT_KEY, 1, VCFHeaderLineType.String, "The highest-impact effect resulting from the current variant (or one of the highest-impact effects, if there is a tie)"),
new VCFInfoHeaderLine(EFFECT_IMPACT_KEY, 1, VCFHeaderLineType.String, "Impact of the highest-impact effect resulting from the current variant " + Arrays.toString(SnpEffConstants.EffectImpact.values())),
new VCFInfoHeaderLine(EFFECT_EXTRA_INFORMATION_KEY, 1, VCFHeaderLineType.String, "Additional information about the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(OLD_NEW_AA_KEY, 1, VCFHeaderLineType.String, "Old/New amino acid for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(OLD_NEW_CODON_KEY, 1, VCFHeaderLineType.String, "Old/New codon for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(CODON_NUM_KEY, 1, VCFHeaderLineType.Integer, "Codon number for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(CDS_SIZE_KEY, 1, VCFHeaderLineType.Integer, "CDS size for the highest-impact effect resulting from the current variant")
);
}
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -133,7 +133,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
validationDataLocation + "1000G.exomes.vcf --snpEffFile " + validationDataLocation +
"snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000",
1,
Arrays.asList("c08648a078368c80530bff004b3157f1")
Arrays.asList("03eae1dab19a9358250890594bf53607")
);
executeTest("Testing SnpEff annotations", spec);
}