public enum OldVariantType extends Enum<OldVariantType>
Enum Constant and Description |
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DOWNSTREAM
Variant is downstream of a gene
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ERROR
Variant assessed as probably erroneous (may indicate an error in the VCF file)
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FS_DELETION
Deletion resulting in a frameshift.
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FS_DUPLICATION
Nucleotide duplication that results in a frameshift.
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FS_INSERTION
Insertion resulting in a frameshift.
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FS_SUBSTITUTION
Nucleotide substitution that results in a frameshift.
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INTERGENIC
variant located between two genes (far enough away not to qualify as upstream/downstream)
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INTRONIC
Variant located in an intron.
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MISSENSE
Variant that leads to the subsitution of one amino acid (note this was earlier "NONYSYNONYMOUS" but the term name
was changed to conform with the terminology od Sequence Ontology).
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ncRNA_EXONIC
Variant located in an exon of a noncoding RNA gene
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ncRNA_INTRONIC
Variant located in an intron of a noncoding RNA gene
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ncRNA_SPLICING
Variant located in a splice site of a noncoding RNA gene
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NON_FS_DELETION
Deletion that does not result in a frameshift.
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NON_FS_DUPLICATION
Nucleotide duplication that does not result in a frameshift.
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NON_FS_INSERTION
Insertion that does not result in a frameshift.
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NON_FS_SUBSTITUTION
Nucleotide substitution that does not result in a frameshift.
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SPLICING
variant located in a splice site
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START_LOSS
Variation leads to the loss of the start codon
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STOPGAIN
Variant that induces a new stop codon (i.e., nonsense)
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STOPLOSS
Variant that alters and removes a wildtype stop codon
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SV_DELETION
Variant is a structual deletion variant 1000bp+
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SV_INSERTION
Variant is a structual insertion variant 1000bp+
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SV_INVERSION
Variant is a structual inversion variant 1000bp+
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SV_SUBSTITUTION
Variant is a structual substitution variant 1000bp+
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SYNONYMOUS
Nucleotide substitution that does not alter the encoded amino acid of the affected codon.
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UPSTREAM
Variant is upstream of a gene
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UTR3
Variant is located in the 3' untranslated region
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UTR5
Variant is located in the 5' untranslated region
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Modifier and Type | Method and Description |
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static OldVariantType[] |
getPrioritySortedList()
This returns an array with the VariantTypes arranged according to their priority.
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boolean |
isTopPriorityVariant()
We do not know, actually, whether any given variant is pathogenic if we just judge its pathogenicity class.
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int |
priorityLevel()
The preference level for annotations is
exonic (1): FS_DELETION, FS_INSERTION, NON_FS_SUBSTITUTION, FS_SUBSTITUTION, MISSENSE,
NON_FS_DELETION, NON_FS_INSERTION, STOPGAIN, STOPLOSS, FS_DUPLICATION, NON_FS_DUPLICATION, START_LOSS,
START_GAIN.
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String |
toDisplayString()
A string representing the variant type (e.g., missense_variant, stop_gained,...)
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String |
toSequenceOntologyID()
Return the sequence ontology accession number for the variant class if available, otherwise return the name.
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String |
toSequenceOntologyTerm()
A Sequence Ontology (SO) term string representing the variant type (e.g., missense_variant, stop_gained,...)
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static OldVariantType |
valueOf(String name)
Returns the enum constant of this type with the specified name.
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static OldVariantType[] |
values()
Returns an array containing the constants of this enum type, in
the order they are declared.
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public static final OldVariantType DOWNSTREAM
public static final OldVariantType FS_DELETION
public static final OldVariantType FS_INSERTION
public static final OldVariantType NON_FS_SUBSTITUTION
public static final OldVariantType FS_SUBSTITUTION
public static final OldVariantType INTERGENIC
public static final OldVariantType INTRONIC
public static final OldVariantType MISSENSE
public static final OldVariantType ncRNA_EXONIC
public static final OldVariantType ncRNA_INTRONIC
public static final OldVariantType ncRNA_SPLICING
public static final OldVariantType NON_FS_DELETION
public static final OldVariantType NON_FS_INSERTION
public static final OldVariantType SPLICING
public static final OldVariantType STOPGAIN
public static final OldVariantType STOPLOSS
public static final OldVariantType SYNONYMOUS
public static final OldVariantType UPSTREAM
public static final OldVariantType UTR3
public static final OldVariantType UTR5
public static final OldVariantType ERROR
public static final OldVariantType NON_FS_DUPLICATION
public static final OldVariantType FS_DUPLICATION
public static final OldVariantType START_LOSS
public static final OldVariantType SV_INSERTION
public static final OldVariantType SV_DELETION
public static final OldVariantType SV_SUBSTITUTION
public static final OldVariantType SV_INVERSION
public static OldVariantType[] values()
for (OldVariantType c : OldVariantType.values()) System.out.println(c);
public static OldVariantType valueOf(String name)
name
- the name of the enum constant to be returned.IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is nullpublic int priorityLevel()
public boolean isTopPriorityVariant()
true
if a variantType has pathogenicity level one, otherwise false
public static OldVariantType[] getPrioritySortedList()
public String toDisplayString()
VariantEffect
public String toSequenceOntologyTerm()
VariantEffect
public String toSequenceOntologyID()
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