Package org.snpeff.vcf
Class VcfConsequence
java.lang.Object
org.snpeff.vcf.VcfConsequence
An 'CSQ' entry in a vcf line ('Consequence' from ENSEMBL's VEP)
Format:
##INFO=invalid input: '<'ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|SYMBOL|SYMBOL_SOURCE|HGNC_ID|BIOTYPE|SIFT|PolyPhen|DOMAINS|HGVSc|HGVSp|GMAF|AFR_MAF|AMR_MAF|ASN_MAF|EUR_MAF|AA_MAF|EA_MAF|CLIN_SIG|SOMATIC|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE">
- Author:
- pablocingolani
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic List
<VcfConsequence> parse
(VcfConsequenceHeader vcfConsequenceHeader, String csqString) static List
<VcfConsequence> parse
(VcfConsequenceHeader vcfConsequenceHeader, VcfEntry ve) toString()
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Field Details
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VCF_INFO_CSQ_NAME
- See Also:
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Constructor Details
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VcfConsequence
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Method Details
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parse
public static List<VcfConsequence> parse(VcfConsequenceHeader vcfConsequenceHeader, String csqString) -
parse
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get
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getConsequence
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getFeature
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getHgvsDna
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getHgvsProt
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toString
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