GA4GH callset

The callset object contains information about an experiment performed on material from a single biosample and is a shared identifier for all variants detected in this experiment, attributed to the referenced biosample.

The schema definitions are done in the YAML file.

Callset

Properties of the Callset class

Property	Type	Format	Description
id	string		The local-unique identifier of this callset (referenced as "callset_id").
biosample_id	string		The identifier ("biosample.id") of the biosample this variant was reported from. This is a shortcut to using the variant -> callset -> biosample chaining.
description	string		A free text description of the callset.
data_use_conditions			Data use conditions applying to data from this callset, as ontology object (e.g. DUO).
geo_provenance			This geo_class attribute ideally describes the geographic location of where this callset was analysed.
info			additional variant information, as defined in the example and accompanying documentation
created	string		The creation time of this record, in ISO8601
updated	string		The time of the last edit of this record, in ISO8601

Extended notes and examples on the Callset properties

---

id

The local-unique identifier of this callset (referenced as “callset_id”).

Example

'id' : "GSM264198"

---

biosample_id

The identifier (“biosample.id”) of the biosample this variant was reported from. This is a shortcut to using the variant -> callset -> biosample chaining.

Example

'biosample_id' : "pgx-bs-987647"

---

description

A free text description of the callset.

Example

'description' : "SNP6 array of cancer sample BRCA-0893"

---

data_use_conditions

Data use conditions applying to data from this callset, as ontology object (e.g. DUO).

Example

'data_use_conditions' : {
  'label' : 'no restriction',
  'id' : 'DUO:0000004'
}

---

geo_provenance

This geo_class attribute ideally describes the geographic location of where this callset was analysed.

Example

'geo_provenance' : {
  'country' : 'Romania',
  'city' : 'Timisoara',
  'latitude' : 45.75,
  'label' : 'Str Marasesti 5, 300077 Timisoara, Romania',
  'longitude' : 21.23
}

---

info

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

Example

'info' : {
  'statusmaps' : {
                    'value' : {
                                 'dupmap' : {
                                               'value' : [
                                                            '',
                                                            '',
                                                            'DUP',
                                                            'DUP',
                                                            'DUP',
                                                            '',
                                                            '',
                                                            '',
                                                            '',
                                                            '',
                                                            ''
                                                          ],
                                               'type' : 'array',
                                               'description' : 'gain cnv status for the corresponding genome intervals
'
                                             },
                                 'binning' : {
                                                'type' : 'number',
                                                'value' : 1000000,
                                                'format' : 'int64',
                                                'description' : 'interval size in bases for the binning, when creating the cnv_maps'
                                              }
                               },
                    'schema' : {
                                  'ref' : './common/Info_class'
                                },
                    'description' : 'The cnv_maps object is a wrapper for genomic interval mapped status information. In Progenetix and arrayMap, this is used to indictate - for fixed 1MB genome intervals - the status (dup_map => "DUP" or "", del_map => "DEL" or ""), or the maximum / minimum positive / negative value encountered in the segment, as far as it has been called to contain DUP or DEL.
With a standard binning of 1MB, the arrays would contain ~3000 values each (depending on genome edition).
'
                  }
}

---

created

The creation time of this record, in ISO8601

Example

'created' : "2017-10-25T07:06:03Z"

---

updated

The time of the last edit of this record, in ISO8601

Example

'updated' : "2022-11-11T09:45:13Z"