UpdateSample - geneyx/geneyx.analysis.api GitHub Wiki

UpdateSampleSequencingQc

This script is used to update the sample level data, such as BAM and Methylation file URLs.

URL:

https://analysis.geneyx.com/api/updateSample

China Domain:

https://fa.shanyint.com/api/updateSample

Action:

POST

Payload:

JSON Structure

Table

Category Parameter Description Required
Auth ApiUserId The API user Id Yes
ApiUserKey The API user key Yes
Sample SerialNumber The VCF serial ID Yes
TakenDate Sample taken date yyyy/mm/dd No
SequenceDate Sample sequencing date yyyy/mm/dd No
ReceivedDate Sample Received Dateyyyy/mm/dd No
Type May be one of the following: RnaSeq, DnaSeq No
Target May be one of the following: WholeGenome, Exome, GenePanel, TargetRegion No
Source May be one of the following: Germline, Tumor, Blood, Buccal, Fetal, Saliva, Other No
Notes Sample Notes No
GenomeBuild Maybe one of the following: hg19, hg38 No
QcData Sample QC Data, such as gene coverage, in JSON format No
BamUrl URL to the BAM file No
MethylationUrl URL to the methylation file No
SubjectName Name of Subject No
SubjectGender M, or F No
SubjectDateOfBirth Date of birth of subject yyyy/mm/dd No
SubjectHasBioSample Bio sample available No
SubjectUseConsentPersonal Personal consent No
SubjectUseConsentClinical Clinical consent No

Example

{
  "SerialNumber": "N_on_hg19.vcf.gz",
  "TakenDate": "2022-12-27T18:56:48.329Z",
  "SequenceDate": "2022-12-27T18:56:48.329Z",
  "ReceivedDate": "2022-12-27T18:56:48.329Z",
  "Type": "string",
  "Target": "string",
  "Source": "string",
  "SequenceMachineId": "string",
  "EnrichmentKitId": "string",
  "Notes": "string",
  "Relation": "string",
  "GenomeBuild": "hg38",
  "BamUrl": "https://xxx.blob.core.windows.net/bam-files/HMC-4.GRCh38.deepvariant.haplotagged.bam",
  "MethylationUrl":"https://xxx.blob.core.windows.net/bam-files/HDS0000013.cpg.bed.gz",
  "ApiUserId": "xxx7TKs2ywINyzv8AUQ==",
  "ApiUserKey": "xxx6d2HA9b5SdVzxEHeY0P2gL4YJnysGKJBhGEFs5vvWWyDuw=="
}

Response

{
    "Code": "success",
    "Data": {
        "PatientId": "347b553e-8c32-4dbc-94a1-ca2507a56c10",
        "Patient": "GAN-6139",
        "SerialNumber": "N_on_hg19.vcf.gz",
        "SequenceMachineId": null,
        "SequenceMachine": null,
        "EnrichmentKitId": "554d962a-3844-420c-951c-3d82818d2e27",
        "EnrichmentKit": "Default - Exons only",
        "EnrichmentKitDescription": "Default - Exons only",
        "TakenDate": "2022-12-27T18:56:48.329Z",
        "SeqDate": "2022-12-27T18:56:48.329Z",
        "ReceivedDate": "2022-12-27T18:56:48.329Z",
        "StatusName": null,
        "Type": null,
        "TypeName": null,
        "Target": 2,
        "TargetName": "Exome",
        "Source": null,
        "SourceName": null,
        "BamUrl": "https://xxx.blob.core.windows.net/bam-files/HMC-4.GRCh38.deepvariant.haplotagged.bam",
        "BamFileExists": false,
        "MethylationUrl": "https://xxx.blob.core.windows.net/bam-files/HDS0000013.cpg.bed.gz",
        "MethylationFileExists": false,
        "CnvNormUrl": null,
        "CnvNormFileExists": false,
        "QcMetricsUrl": null,
        "QcMetricsFileExists": false,
        "ErrorDescription": null,
        "Notes": "string",
        "QcData": null,
        "SeqQcData": null,
        "Relation": 0,
        "RelationName": "Self",
        "GenomeBuild": 1,
        "GenomeBuildName": "hg38",
        "SeqSampleId": null,
        "Assignment": {
            "UserId": null,
            "FullName": null,
            "Name": null,
            "Email": null,
            "AssignedBy": null,
            "AssignDate": "0001-01-01T00:00:00",
            "GroupCodes": [],
            "Groups": []
        },
        "Files": [
            {
                "ID": "78a3d9c2-89b5-4654-9664-359fe36c4659",
                "FileTypeName": "SNV",
                "FileType": 1,
                "FileSubType": null,
                "FileName": "N_on_hg19.vcf.gz",
                "CreateDate": "2025-01-07T10:30:14.55",
                "TotalVariants": 2
            }
        ],
        "NewFiles": null,
        "ExcludeFromLAF": false,
        "LatestVS": "",
        "RunPgx": false,
        "ID": "438c82ca-263a-4c55-ad01-1cd7bcf5b9d9",
        "CreatedByUser": "Eldar Dedic",
        "CreateDate": "2025-01-07T10:30:14.55",
        "ModifiedByUser": "Geneyx Support",
        "ModifyDate": "2025-01-08T23:26:15.0079452Z"
    },
    "Info": null,
    "MoreInfo": null,
    "NeedEval": false
}
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