id String | The clinical analysis ID. |
uuid String | A universally unique identifier for the clinical analysis. |
description String | The clinical analysis description. |
type Type | The type of the clinical analysis: | SINGLE |
| | FAMILY |
| | CANCER |
| | COHORT |
| | AUTOCOMPARATIVE |
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disorder Disorder | Disorder. id String | The disorder ID. | name String | The disorder name. | source String | The source or database for that disorder. | description String | The disorder description. | evidences List<Phenotype> | List of phenotypes related to the disorder. ageOfOnset String | Age at which the proband acquired a condition or symptoms of a that disorder. | status Status | Status. | OBSERVED |
| | NOT_OBSERVED |
| | UNKNOWN |
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| attributes Map<String, Object> | Attributes. |
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files List<File> | List of files with all VCF, BAM, ... used in this analysis.
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proband Individual | Proband individual. |
family Family | Family info, only exist when analysis type is FAMILY. |
roleToProband Map<String, familiarRelationship> | Familiar relationship: | MOTHER | Mother. | | FATHER | Father. | | STEP_MOTHER | Mother. | | STEP_FATHER | Father. | | IDENTICAL_TWIN | Twin. | | FRATERNAL_TWIN | Twin. | | FULL_SIBLING | Sibling. | | HALF_SIBLING | Sibling. | | STEP_SIBLING | Sibling. | | SISTER | Sister. | | BROTHER | Brother. | | STEP_SISTER | Sister. | | STEP_BROTHER | Brother. | | SON | Son. | | DAUGHTER | Daughter. | | CHILD_OF_UNKNOWN | Child. | | UNCLE | Uncle. | | AUNT | Aunt. | | MATERNAL_AUNT | Aunt. | | MATERNAL_UNCLE | Uncle. | | PATERNAL_AUNT | Aunt. | | PATERNAL_UNCLE | Uncle. | | NEPHEW | Nephew. | | NIECE | Niece. | | GRANDFATHER | Grandfather. | | GRANDMOTHER | Grandmother. | | MATERNAL_GRANDMOTHER | Grandmother. | | PATERNAL_GRANDMOTHER | Grandmother. | | MATERNAL_GRANDFATHER | Grandfather. | | PATERNAL_GRANDFATHER | Grandfather. | | GREAT_GRANDFATHER | Great-grandfather. | | GREAT_GRANDMOTHER | Great-grandmother. | | DOUBLE_FIRST_COUSIN | Cousin. | | COUSIN | Cousin. | | MALE_COUSIN | Cousin. | | FEMALE_COUSIN | Cousin. | | SECOND_COUSIN | Cousin. | | MALE_SECOND_COUSIN | Cousin. | | FEMALE_SECOND_COUSIN | Cousin. | | SPOUSE | Spouse. | | HUSBAND | Husband. | | OTHER | Other. | | UNKNOWN | Unknown. | | UNRELATED | Unrelated. | | PROBAND | Proband. |
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qualityControl ClinicalAnalysisQc | Quality control. quality Enum | Quality control result. | HIGH | QC passed. | | MEDIUM | Uncertainty. | | LOW | QC failed. | | UNKNOWN | QC not assessed. |
| variant VariantQc | Quality control on variant data. stats List<SampleVariantStats> | Sample variant stats. See sample variant stats data model. | files List<File> | List of files related to this sampleId the variant data, e.g.: images. |
| alignment AlignmentQc | Quality control on variant data. stats List<AlignmentStats> | Alignment stats for each alignment file (BAM). See alignment stats data model schema. | files List<File> | List of files related to the variant data, , e.g.: images. | geneCoverageStats LIst<GeneCoverageStats>
| Gene coverage stats for each alignment file (BAM). fileId String | File ID. | sampleId String | Sample ID. | gene String | Gene name. | stats List<TranscriptCoverageStats> | id String | Transcript ID. | name String | Transcript name. | biotype String | Transcript biotype. | chromosome String | Chromosome where the transcript is located. | start int | Position where the transcript starts. | end int | Position where the transcript ends. | length int | The transcript length as the sum of the lengths of its exons. | depths Double[10] | % coverage for 1x, 5x, 10x, 15x, 20x, 25x, 30x, 40x, 50x, 60x, 75x and 100x | lowCoverageThreshold int | Regions under this coverage depth threshold will be reported in the list lowCoverageRegions. Default value: 30. | lowCoverageRegionStats List<LowCoverageRegionStats> | Statistics for regions whose coverage depth is under the value lowCoverageThreshold. chromosome String | Chromosome. | start int | Region start position. | end int | Region end position | depthAvg double | Average depth. | depthMin int | Minimum depth. |
| exonStats List<ExonCoverageStats> | Statistics for each exon in the transcript. id String | Exon ID. | chromosome String | Chromosome. | start int | Region start position. | end int | Region end position | depthAvg double | Average depth. | depthMin int | Minimum depth. | depthMax int | Maximum depth. |
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| analyst Analyst | Analyst carrying out the QC. name String | Name. | email String | E-mail. | company String | Company. |
| date Date | Modification date. | comments List<Comment> | Comments. author String | Author. | type String | Type. | message String | Message. | date String | Date. |
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interpretation Interpretation | Primary interpretation. See the interpretation data model schema.
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secondaryInterpretations List<Interpretation> | List of secondary interpretations. See the interpretation data model schema. |
consent ClinicalConsent | Consent. primaryFindings ConsentStatus | Consent for primary findings. | YES | Yes. | | NO | No. | | UNKNOWN | Unknown. |
| secondaryFindings ConsentStatus | Consent for secondary findings. | YES | Yes. | | NO | No. | | UNKNOWN | Unknown. |
| carrierFindings ConsentStatus | Consent for carrier findings. | YES | Yes. | | NO | No. | | UNKNOWN | Unknown. |
| researchFindings ConsentStatus | Consent for research findings. | YES | Yes. | | NO | No. | | UNKNOWN | Unknown. |
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analyst ClinicalAnalysisAnalyst | Information about the analyst. responsible String | Analyst. | assignedBy String | A person who assigned the analyst. | date String | Date. |
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priority Priority | Priority. |
flags List<String> | List of flags. |
status CustomStatus | Clinical analysis status set by the user: name String | Name. | description String | Description. | date String | Date. |
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creationDate String | Creation date. |
modificationDate String | Modification date. |
dueDate String | Due date. |
release int | Release. |
comments List<Comment> | List of comments. author String | Author. | type String | Type. | message String | Message. | date String | Date. |
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report ClinicalAnalysisReport | Clinical analysis report. |
alerts List<Alert> | List of alerts. author String | Author. | date String | Date. | message String | Message. | risk Risk | Risk. |
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internal ClinicalAnalysisInternal | Internal information. status ClinicalAnalysisStatus | Clinical analysis internal status: name String | Name. | INCOMPLETE |
| | READY |
| | DELETED |
| | READY_FOR_VALIDATION |
| | READY_FOR_INTERPRETATION |
| | INTERPRETATION_IN_PROGRESS |
| | READY_FOR_INTERPRETATION_REVIEW |
| | INTERPRETATION_REVIEW_IN_PROGRESS |
| | READY_FOR_REPORT |
| | REPORT_IN_PROGRESS |
| | DONE |
| | REVIEW_IN_PROGRESS |
| | CLOSED |
| | REJECTED |
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| description String | Description. | date String | Date. |
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attributes Map<String, Object> | Map of attributes. |