VariantCall class

A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named rs1234 in a call set with the name NA12345.

Constructors

VariantCall()
VariantCall.fromJson(Map _json)

Properties

callSetId ↔ String
The ID of the call set this variant call belongs to.
read / write
callSetName ↔ String
The name of the call set this variant call belongs to.
read / write
genotype ↔ List<int>
The genotype of this variant call. Each value represents either the value of the referenceBases field or a 1-based index into alternateBases. If a variant had a referenceBases value of T and an alternateBases value of ["A", "C"], and the genotype was [2, 1], that would mean the call represented the heterozygous value CA for this variant. If the genotype was instead [0, 1], the represented value would be TA. Ordering of the genotype values is important if the phaseset is present. If a genotype is not called (that is, a . is present in the GT string) -1 is returned.
read / write
genotypeLikelihood ↔ List<double>
The genotype likelihoods for this variant call. Each array entry represents how likely a specific genotype is for this call. The value ordering is defined by the GL tag in the VCF spec. If Phred-scaled genotype likelihood scores (PL) are available and log10(P) genotype likelihood scores (GL) are not, PL scores are converted to GL scores. If both are available, PL scores are stored in info.
read / write
info ↔ Map<String, List<Object>>
A map of additional variant call information. This must be of the form map<string, string[]> (string key mapping to a list of string values). [...]
read / write
phaseset ↔ String
If this field is present, this variant call's genotype ordering implies the phase of the bases and is consistent with any other variant calls in the same reference sequence which have the same phaseset value. When importing data from VCF, if the genotype data was phased but no phase set was specified this field will be set to *.
read / write
hashCode → int
The hash code for this object.
read-only, inherited
runtimeType → Type
A representation of the runtime type of the object.
read-only, inherited

Methods

toJson() → Map<String, Object>
noSuchMethod(Invocation invocation) → dynamic
Invoked when a non-existent method or property is accessed.
inherited
toString() → String
Returns a string representation of this object.
inherited

Operators

operator ==(dynamic other) → bool
The equality operator.
inherited