Variant progenetix

{S}[B] Status [i]
playground
Provenance
Used by
Contributors
Source (v2020-02-12)

Attributes

Type: object
Description: The Progenetix Variant represents a non-tracking version of the Beacon definition.

The document describes attributes of the BeaconGenomicVariant object. In its current implementation, BeaconGenomicVariant (and related genomic objects such as callset) represent extended versions of the original, VCF-derived GA4GH variant schema.

Compared to the VCF model it was derived from, this schema includes some changes:

This format may be superseeded or augmented based on current developments in the GA4GH::GKS work stream.

Properties

Property Type
alternateBases array of string
biosampleId string
callsetId string
digest string
end array of int64
genotype array of string
id string
info object
mateName https://schemablocks.org/schemas/beacon/v1.1.0/Chromosome.json [SRC] [HTML]
referenceBases string
referenceName https://schemablocks.org/schemas/beacon/v1.1.0/Chromosome.json [SRC] [HTML]
start array of int64
variantType string

alternateBases

TODO: Redefine for single-allele use?

alternateBases Value Examples
[
   "C"
]
[
   "TA",
   "TAA"
]

biosampleId

The optional identifier (“biosample.id”) of the biosample this variant was reported from. This is a shortcut to variant -> callset -> biosample chaining or replaces this in data models w/o separate callset level.

biosampleId Value Example
"pgx-bs-987647"

callsetId

callsetId Value Example
"PGX_AM_CS_GSM1690424"

digest

digest Value Example
"4:12282-46465:DEL"

end

array of 0 (for presise sequence variants), 1 or 2 (for imprecise end position of structural variant) integers

end Value Example
[
   "21977798",
   "21978106"
]

genotype

The genotype parameter is largely redundant for single-sample variant annotations in contrast to VCF, where the alternat_bases calls have to be indicated for multiple callsets.

TODO: Remove for single-allele definition of BeaconGenomicVariant?

genotype Value Examples
[
   "1",
   "."
]
[
   "2",
   "1"
]

id

id Value Example
"amvar-8754-7751-1119-8539"

info

additional variant information, as defined in the example and accompanying documentation

info Value Example
{
   "cnv_length" : "1205290",
   "cnv_value" : "-0.294"
}

mateName

Mate name (chromosome) for fusion (BND) events; otherwise left empty. Accepting values 1-22, X, Y. Compared to the VCF specification, where a fusion is defined from 2 BND variants and verbose annotations for describing fusion partners, the use of the mate_name attribute allows to treat fusion events as single “variant”. Conventions:

mateName Value Examples
"14"
"18"

referenceBases

one or more bases at start position in the reference genome, which have been replaced by the alternate_bases value

referenceBases Value Example
"G"

referenceName

Chromosome as string

referenceName Value Examples
"22"
"Y"

start

array of 1 or 2 (for imprecise end position of structural variant) integers

start Value Example
[
   "20867740"
]

variantType

the variant type in case of a named (structural) variant (e.g. DUP, DEL, BND …)

variantType Value Example
"DEL"

Variant Value Examples

{
   "alternate_bases" : [
      "AC",
      "ACC"
   ],
   "callset_id" : "DIPG_CS_0290",
   "digest" : "2:203420136:A>AC,ACC",
   "genotype" : [
      "2",
      "1"
   ],
   "id" : "5be1840772798347f0ed9e8b",
   "reference_bases" : "A",
   "reference_name" : "2",
   "start" : [
      "203420136"
   ]
}
{
   "biosample_id" : "fcl-bs-0099615",
   "callset_id" : "structdb-cs-nhl-0009876",
   "digest" : "8,14:20867740-21977798,21978106:BND",
   "end" : [
      "21977798",
      "21978106"
   ],
   "id" : "structdb-var-123456789",
   "mate_name" : "14",
   "reference_bases" : "N",
   "reference_name" : "8",
   "start" : [
      "20867740"
   ],
   "variant_type" : "BND"
}
{
   "callset_id" : "structdb-cs-nhl-0009876",
   "digest" : "6:63450000,63550000-63450000,63550000:DEL",
   "end" : [
      "63450000",
      "63550000"
   ],
   "id" : "structdb-var-123456790",
   "info" : {
      "cnv_length" : "85500000",
      "cnv_value" : "-0.294"
   },
   "reference_bases" : "N",
   "reference_name" : "6",
   "start" : [
      "63450000",
      "63550000"
   ],
   "variant_type" : "DEL"
}
2020-06-23