All Implemented Interfaces:

Serializable, Comparable<VariantContext.Type>

Enclosing class:

VariantContext

public static enum VariantContext.Type
extends Enum<VariantContext.Type>

See Also:

NCBI Handbook

Format:

• dbSNP variation class
• Rules for assigning allele classes
• Sample allele definition

Supported Types

• Single Nucleotide Polymorphisms (SNPs)a
• Strictly defined as single base substitutions involving A, T, C, or G.
• A/T

• Deletion/Insertion Polymorphisms (DIPs)
• Designated using the full sequence of the insertion as one allele, and either a fully defined string for the variant allele or a '-' character to specify the deleted allele. This class will be assigned to a variation if the variation alleles are of different lengths or if one of the alleles is deleted ('-').
• T/-/CCTA/G

• No-variation
• Reports may be submitted for segments of sequence that are assayed and determined to be invariant in the sample.
• (NoVariation)

• Mixed
• Mix of other classes

Also supports NO_VARIATION type, used to indicate that the site isn't polymorphic in the population

Not currently supported:

• Heterozygous sequence
• The term heterozygous is used to specify a region detected by certain methods that do not resolve the polymorphism into a specific sequence motif. In these cases, a unique flanking sequence must be provided to define a sequence context for the variation.
• (heterozygous)

• Microsatellite or short tandem repeat (STR)
• Alleles are designated by providing the repeat motif and the copy number for each allele. Expansion of the allele repeat motif designated in dbSNP into full-length sequence will be only an approximation of the true genomic sequence because many microsatellite markers are not fully sequenced and are resolved as size variants only.
• (CAC)8/9/10/11

• Named variant
• Applies to insertion/deletion polymorphisms of longer sequence features, such as retroposon dimorphism for Alu or line elements. These variations frequently include a deletion '-' indicator for the absent allele.
• (alu) / -

• Multi-Nucleotide Polymorphism (MNP)
• Assigned to variations that are multi-base variations of a single, common length
• GGA/AGT