VariantCalls
Summary of SMaHT Portal object type VariantCalls . Its parent type is: SubmittedFile. Property names in red are required properties; those in blue are identifying properties; and properties with types in green are reference properties.Description: Files containing variant calls.
Tip
See actual VariantCalls data hereRequired Properties
| Property | Type | Description |
|---|---|---|
| data_category | array of enum | See below for more details. |
| data_type | array of enum | See below for more details. |
| file_format | FileFormat string | See below for more details. See values here |
| file_sets | FileSet array of string | See below for more details. |
| filename | string | See below for more details. |
| reference_genome | ReferenceGenome string | See below for more details. See values here |
| submission_centers | SubmissionCenter array of string | See below for more details. See values here |
| submitted_id | string | See below for more details. |
Identifying Properties
| Property | Type | Description |
|---|---|---|
| accession | string | See below for more details. |
| submitted_id | string | See below for more details. |
| uuid | string | See below for more details. |
Reference Properties
| Property | Type | Description |
|---|---|---|
| analytes | Analyte array of string | See below for more details. |
| assays | Assay array of string | See below for more details. |
| consortia | Consortium array of string | See below for more details. See values here |
| derived_from | File array of string | See below for more details. |
| donors | Donor array of string | See below for more details. |
| external_quality_metrics | ExternalQualityMetric array of string | See below for more details. |
| file_format | FileFormat string | See below for more details. See values here |
| file_sets | FileSet array of string | See below for more details. |
| libraries | Library array of string | See below for more details. |
| meta_workflow_run_inputs | MetaWorkflowRun array of string | See below for more details. |
| meta_workflow_run_outputs | MetaWorkflowRun array of string | See below for more details. |
| quality_metrics | QualityMetric array of string | See below for more details. |
| reference_genome | ReferenceGenome string | See below for more details. See values here |
| sample_sources | Tissue array of string | See below for more details. |
| samples | Sample array of string | See below for more details. |
| sequencing | Sequencing array of string | See below for more details. |
| sequencing_center | SubmissionCenter string | See below for more details. See values here |
| software | Software array of string | See below for more details. |
| submission_centers | SubmissionCenter array of string | See below for more details. See values here |
Properties
| Property | Type | Description |
|---|---|---|
| access_status • Open • Protected | enum of string | Access status for the file contents. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| annotated_filename | string • unique | Filename containing controlled metadata. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| comparator_description | string | Description of comparator sample files used for normal matching. |
| consortia | Consortium • array of string • unique | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Germline Variant Calls • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_generation_summary . target_read_count | array of string | - |
| data_type • CNV • Indel • MEI • SNV • SV | array of enum • min items: 1 • unique | - |
| dataset • colo829_snv_indel_challenge_data • colo829bl • colo829blt_50to1 • colo829blt_in_silico • colo829t • hapmap • hapmap_snv_indel_challenge_data • hg002 • hg00438 • hg005 • hg02257 • hg02486 • hg02622 • ipsc_snv_indel_challenge_data • lb_fibroblast • lb_ipsc_1 • lb_ipsc_2 • lb_ipsc_4 • lb_ipsc_52 • lb_ipsc_60 • mei_detection_challenge_data • tissue | enum of string | Dataset associated with the file. |
| derived_from | File • array of string • min items: 1 • unique | Link to files used as input to create this file. |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_databases | array of string | External databases used for filtering variant calls. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| extra_files_creds | object • calculated | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_sets | FileSet • array of string • min items: 1 • unique | Link to file sets associated with this file. |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| filtering_methods | array of string | Filtering methods used in variant calling. |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| mode • Paired • Single Sample | enum of string | Mode used for variant calling. |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| override_group_coverage | number • min value: 0 | - |
| override_release_tracker_description | string • min value: 0 | - |
| override_release_tracker_title | string • min value: 0 | - |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| reference_genome | ReferenceGenome • string | Reference genome used for alignment. See values here |
| release_tracker_description | string • calculated | - |
| release_tracker_title | string • calculated | - |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissue_details | array of string | - |
| sample_summary . tissue_subtypes | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| software | Software • array of string • min items: 1 • unique | Link to software used to create this file. |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_VARIANT-CALLS_[A-Z0-9-_.]{4,}$ |
| submitted_md5sum | string • format: hex | Submitted MD5 checksum of the file. |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |