class Google::Apis::GenomicsV1::VariantCall
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.
Attributes
The ID of the call set this variant call belongs to. Corresponds to the JSON property `callSetId` @return [String]
The name of the call set this variant call belongs to. Corresponds to the JSON property `callSetName` @return [String]
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 `[ āAā, āCā]`, 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. Corresponds to the JSON property `genotype` @return [Array<Fixnum>]
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`. Corresponds to the JSON property `genotypeLikelihood` @return [Array<Float>]
A map of additional variant call information. This must be of the form map ( string key mapping to a list of string values). Corresponds to the JSON property `info` @return [Hash<String,Array<Object>>]
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 `*`. Corresponds to the JSON property `phaseset` @return [String]
Public Class Methods
# File generated/google/apis/genomics_v1/classes.rb, line 3007 def initialize(**args) update!(**args) end
Public Instance Methods
Update properties of this object
# File generated/google/apis/genomics_v1/classes.rb, line 3012 def update!(**args) @call_set_id = args[:call_set_id] if args.key?(:call_set_id) @call_set_name = args[:call_set_name] if args.key?(:call_set_name) @genotype = args[:genotype] if args.key?(:genotype) @phaseset = args[:phaseset] if args.key?(:phaseset) @genotype_likelihood = args[:genotype_likelihood] if args.key?(:genotype_likelihood) @info = args[:info] if args.key?(:info) end