Input File for Sample Metadata Manifest
The input file for a sample metadata manifest requires the following columns:
| • | Sample ID—A unique ID for the analysis result, up to 100 characters. |
| • | Result Path—A unique, system-generated ID for the analysis result. |
| • | Subject ID—A unique ID for the sample donor, up to 100 characters. |
| • | Sample Class—Determines a germline or tumor analysis. Acceptable values are germline, tumor, tumor-only, and tumor-normal (values are not case-sensitive). |
NOTE
Tumor sample class values appear as Tumor-only in the Registry table.
The following additional columns are optional input:
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Column |
Description |
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Project ID |
The unique ID for the project, up to 100 characters. |
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Mother ID |
The unique ID for the mother of the subject, up to 100 characters. |
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Father ID |
The unique ID for the father of the subject, up to 100 characters. |
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Sex |
The biological sex of the subject, male or female (case-insensitive). Alternatively, 1 for male or 2 for female. This column is recommended. The software requires an assigned sex to view the Variants table. |
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Affection Status |
Indicates whether the disease affects the subject. The case-insensitive values of affected and unaffected are acceptable. Alternatively, use the PED format:
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Indication |
The indication for the presence of disease, up to 150 characters. Data in this column are imported as phenotypes with an ontology source of Other. |
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Matched normal Sample ID |
A sample ID for the matched normal sample for a tumor sample. A matched normal sample is unaffected tissue from a subject who has a tumor. |
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Sample Type |
The primary sample type. The following acceptable values are case-insensitive:
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Phenotype |
The phenotypes associated with the sample. Enter the HPO or SNOMED-CT codes for each phenotypes, separated by a comma. |
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Tumor Type |
The type of tumor associated with the sample. Enter the SNOMED code for the tumor type. |
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Primary or Metastasis* |
The tumor site, primary or metastasis (case-insensitive). |
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Sample harvest site* |
The location of tumor sample extraction, up to 200 characters. |
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Pathologist Tumor Purity Assessment* |
The purity of the tumor sample, on a scale of 0–1, based on the evaluation of the pathologist. Up to two decimal places are allowed. |
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Assembly |
The associated reference genome build. The values hg19, GRCH37, or GRCH38 are acceptable. |
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Comments |
General notes about the analysis result, up to 500 characters. |
*Applies to tumor only.