CSV format requirements

General CSV format requirements

The following are the general format requirements for a CSV file used to create multiple cases:

  1. The file must have a .csv extension.

  2. The file must contain a [Data] header.

  3. The row after [Data] header must include the field names identifying the data in each column. The column names are case-sensitive.

  4. The row after the column name header and each subsequent row represents a sample.

  5. Each column represents a data field.

  6. It is essential that there are no empty rows between the [Data] header and the last sample row.

  7. Number of cases per file can’t be greater than 50.

  8. On versions before 34.0, cells should not contain commas. Consider replacing the commas with semicolons.


CSV schema

1. Mandatory fields

Must be present in the sample table at all times.

  1. Case Type;

  2. Family Id;

  3. Phenotypes OR Phenotypes Id.

2. Conditionally mandatory fields

If these fields are left empty, it will result in the creation of an empty sample.

  1. BioSample Name;

  2. Files Names;

  3. Storage Provider Id;

This field is mandatory if Files Names is empty:

  1. Sample Type.

This field is required if the "auto" option is used for Files Names (only relevant for BSSH):

  1. Default Project.

3. Optional fields

The sample table may include these supported optional columns.

  1. Boost Genes;

  2. Clinical Notes;

  3. Date Of Birth;

  4. Due Date;

  5. Execute now;

  6. Gender;

  7. Gene List Id;

  8. Kit Id;

  9. Label Id;

  10. Opt In;

  11. Relation;

  12. Selected Preset;

  13. Visualization Files.

4. Custom fields

The sample table may contain custom columns to suit your specific needs and include any relevant information that is important for your workflow.

Each custom field must be assigned a unique name without spaces. Data from custom columns is saved per case under the Additional information section of Case Info.

Note: In cases with more than one sample, custom fields are only recognized and added to case information if their values appear within the same table row where the Relation field is equal to "proband".

Custom field examples:


Batch case .csv file validation rules

Mandatory (highlighted in red), Conditionally mandatory (highlighted in orange), and Optional fields should be filled in according to the following rules.

*Required BSSH file path format:

For BSSH, it is necessary to use the actual names (numbers):

/projects/3824821/appresults/2319318/files/119675608

instead of aliases

/projects/ABC_DEF_2022-12-22_DEv395/appresults/ABC-GM58342-def/files/ABC-GM58342-def.hard-filtered.vcf.gz

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