class Google::Apis::GenomicsV1::Variant

A variant represents a change in DNA sequence relative to a reference sequence. For example, a variant could represent a SNP or an insertion. Variants belong to a variant set. For more genomics resource definitions, see [Fundamentals of Google Genomics](cloud.google.com/genomics/fundamentals-of-google- genomics) Each of the calls on a variant represent a determination of genotype with respect to that variant. For example, a call might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related calls typically from one sample.

Attributes

alternate_bases[RW]

The bases that appear instead of the reference bases. Corresponds to the JSON property `alternateBases` @return [Array<String>]

calls[RW]

The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant. Corresponds to the JSON property `calls` @return [Array<Google::Apis::GenomicsV1::VariantCall>]

created[RW]

The date this variant was created, in milliseconds from the epoch. Corresponds to the JSON property `created` @return [String]

end[RW]

The end position (0-based) of this variant. This corresponds to the first base after the last base in the reference allele. So, the length of the reference allele is (end - start). This is useful for variants that don't explicitly give alternate bases, for example large deletions. Corresponds to the JSON property `end` @return [String]

filter[RW]

A list of filters (normally quality filters) this variant has failed. `PASS` indicates this variant has passed all filters. Corresponds to the JSON property `filter` @return [Array<String>]

id[RW]

The server-generated variant ID, unique across all variants. Corresponds to the JSON property `id` @return [String]

info[RW]

A map of additional variant 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>>]

names[RW]

Names for the variant, for example a RefSNP ID. Corresponds to the JSON property `names` @return [Array<String>]

quality[RW]

A measure of how likely this variant is to be real. A higher value is better. Corresponds to the JSON property `quality` @return [Float]

reference_bases[RW]

The reference bases for this variant. They start at the given position. Corresponds to the JSON property `referenceBases` @return [String]

reference_name[RW]

The reference on which this variant occurs. (such as `chr20` or `X`) Corresponds to the JSON property `referenceName` @return [String]

start[RW]

The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases. Corresponds to the JSON property `start` @return [String]

variant_set_id[RW]

The ID of the variant set this variant belongs to. Corresponds to the JSON property `variantSetId` @return [String]

Public Class Methods

new(**args) click to toggle source
# File generated/google/apis/genomics_v1/classes.rb, line 2931
def initialize(**args)
   update!(**args)
end

Public Instance Methods

update!(**args) click to toggle source

Update properties of this object

# File generated/google/apis/genomics_v1/classes.rb, line 2936
def update!(**args)
  @variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
  @id = args[:id] if args.key?(:id)
  @names = args[:names] if args.key?(:names)
  @created = args[:created] if args.key?(:created)
  @reference_name = args[:reference_name] if args.key?(:reference_name)
  @start = args[:start] if args.key?(:start)
  @end = args[:end] if args.key?(:end)
  @reference_bases = args[:reference_bases] if args.key?(:reference_bases)
  @alternate_bases = args[:alternate_bases] if args.key?(:alternate_bases)
  @quality = args[:quality] if args.key?(:quality)
  @filter = args[:filter] if args.key?(:filter)
  @info = args[:info] if args.key?(:info)
  @calls = args[:calls] if args.key?(:calls)
end