Field description type properties example enum
alternateBases Alternate bases for this variant (starting from start). Accepted values: IUPAC codes for nucleotides (e.g. 'https://www.bioinformatics.org/sms/iupac.html'). N is a wildcard, that denotes the position of any base, and can beused as a standalone base of any type or within a partially knownsequence. As example, a query of ANNT the Ns can take take any form of[ACGT] and will match ANNT, ACNT, ACCT, ACGT ... and so forth. an empty value is used in the case of deletions with the maximally trimmed, deleted sequence being indicated in ReferenceBases Categorical variant queries, e.g. such not being represented through sequence & position, make use of the variantType parameter. either alternateBases or variantType is required. string NA NA NA
caseLevelData array NA NA NA
frequencyInPopulations NA array NA NA NA
identifiers NA NA NA NA NA
molecularAttributes NA NA NA NA NA
position This section groups all attributes that allows to 'identify' a variant via its position in the genome. object assemblyId,end,refseqId,start NA NA
referenceBases Reference bases for this variant (starting from start). * Accepted values: IUPAC codes for nucleotides (e.g. 'https://www.bioinformatics.org/sms/iupac.html'). N is a wildcard, that denotes the position of any base, and can be used as a standalone base of any type or within a partially known sequence. As example, a query of ANNT the Ns can take take any form of [ACGT] and will match ANNT, ACNT, ACCT, ACGT ... and so forth. * an empty value is used in the case of insertions with the maximally trimmed, inserted sequence being indicated in AlternateBases. NOTE: Many Beacon instances could not support UIPAC codes and it is not mandatory for them to do so. In such cases the [ACGTN] is mand string NA NA NA
variantInternalId Reference to the variant ID (internal ID). This is no a public Id, but the 'primary key/identifier' of that variant inside a given Beacon instance. Therefore, different Beacon instances could have a variantInternalId = 1 and they could refer to completely unrelated variants. The public, standard, popular identifiers or the GA4GH Variant Representation Id (VRSid) MUST be returned in the 'identifiers' section. A Beacon instance can, of course, use the VRSid as their own internal id, in such case, the VRSid would be repeated in both places. string NA NA NA
variantLevelData NA NA NA NA NA
variantType The variantType declares the nature of the variation in relation to a reference. It could be a single change, a short insertion or deletion, a bigger structural change, etc. In a response, it is used to describe the variation. In a request, it is used to declare the type of event the Beacon client is looking for. It could be used standalone (without alternateBases parameter) in cases in which query variants could not be defined through a sequence of one or more bases. Examples here are e.g. structural variants: * DUP - increased allelic count of material from the genomic region between start and end positions - no assumption about the placement of the additional sequences is being made (i.e. no in situ requirement as tandem duplications) * DEL: deletion of sequence following start * BND: breakend, i.e. termination of the allele at position start or in the start[0]] => start[1] interval, or fusion of the sequence to distant partner. Either alternateBases or variantType is required, with the exception of range queries (single start and end parameters). string NA NA NA