CSV format requirements for case upload

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.

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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. Assignee ID (v100.40.0+)
2. Boost Genes
3. Clinical Notes
4. Date Of Birth
5. Due Date
6. Execute now
7. Gender. See an important note
8. Gene List Id
9. Intersect Bed Id (v38.0+)
10. Kit Id
11. Label Id
12. Opt In
13. Relation
14. Selected Preset. See an important note
15. 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:

Field (column) name	Field details	Expected input	Example
Institution	Custom	Free text	GenoMed Solutions
Sample_Received_Date	Custom	Free text	24-02-2022
Sample_Type	Custom	Free text	Amniotic Fluid

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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.

Field (column) name	Field details	Expected input	Example
Assignee ID (v100.40.0+)	Optional. Users subscribed to case updates. Appears as Participants in the Case info tab and the Cases table.	Comma-separated list of user IDs	3,10,14
BioSample Name	Conditionally mandatory. An empty sample will be created if the field is left blank.	Free text	NA24385
Boost Genes	Optional. Indicates whether the Boost genes mode will be used. TRUE means that variants in the targeted genes will receive upgraded scores during prioritization by the AI Shortlist algorithm. Default value is FALSE. Only considered for proband.	1. TRUE 2. FALSE	TRUE
Case Type	Mandatory. Only considered for proband.	1. Whole Genome 2. Exome 3. Custom Panel 4. Array 5. Custom case type	Whole Genome
Clinical Notes	Optional	Free text	A 14-year-old boy with a visual acuity of 20/200 in both eyes in whom hearing loss was first noted at 5 years of age on routine screening; audiometry revealed sensorineural hearing loss.
Date Of Birth	Optional	YYYY-MM-DD	2013-01-22
Default Project	Conditionally mandatory. Must be filled in if the auto option is used for Files Names (only relevant for BSSH).	Free text	GIAB
Due Date	Optional	YYYY-MM-DD	2023-05-03
Execute now	Optional. Default value is TRUE. Use FALSE if you don’t want to run the case upon uploading the file. Only considered for proband.	1. TRUE 2. FALSE	FALSE
Family Id	Mandatory	Free text	RM8392
Files Names	Conditionally mandatory. An empty sample will be created if the field is left blank. The existing option automatically locates FASTQ files based on the BioSample Name. Note: If data files for an existing case were sourced from the customer’s external bucket and later removed, attempting to create a case from those files will result in an error. Learn about the current limitation for CRAM file input. With the auto option, BSSH users can automatically locate FASTQ files based on the BioSample Name and Default Project provided. When using BSSH without the auto option, ensure that your file path is formatted correctly.	1. Semicolon-separated list of paths to .fastq, .fastq.gz, .vcf, .vcf.gz, .bam, .cram, .gt_sample_summary.json, .annotated_cyto.json files without spaces 2. existing 3. auto (BSSH)	/GIAB_cases/1/NA24385.dragen.hard-filtered.gvcf.gz;/QA_cases/Other/NA24385.dragen.cnv.vcf.gz;/QA_cases/Other/NA24385.dragen.repeats.vcf;
Gender	Optional. Default value is U. See an important note.	1. F 2. M 3. U	M
Gene List Id	Optional. Must be the id of a previously defined Gene List. Only considered for proband.	Integer	12345
Kit Id	Optional. <38.0: ID of a Region of interest BED. 38.0+: ID of a Coverage BED. Must be the id of a previously defined kit. Only considered for proband.	Integer	23456
Intersect Bed Id (v38.0+)	Optional. ID of a Region of interest BED. Must be the id of a previously defined kit. Only considered for proband.	Integer	78957
Label Id	Optional. Must be the id of a previously defined Case Label. Only considered for proband.	Integer	34567
Opt In	Optional. Indicates whether the case subject consented to the extended sharing of data with your network(s). Default value is TRUE.	1. TRUE 2. FALSE	FALSE
Phenotypes	Mandatory for proband sample if Phenotypes Id is empty. List must be under 100. It is possible to include non-HPO terms if Phenotypes Id is empty.	Semicolon-separated list of HPO phenotype terms Unaffected is used for non-affected family members.	Abnormal pupillary function;Orthotopic os odontoideum;
Phenotypes Id	Mandatory for proband sample if Phenotypes is empty. List must be under 100.	Semicolon-separated list of HPO phenotype IDs	HP:0007686;HP:0025375;
Relation	Optional. Default value is proband. Values proband, father, mother can be only used once per Family ID. One sample with Relation proband is required per Family ID.	1. proband 2. mother 3. father 4. sibling	mother
Sample Type	Conditionally mandatory. Required if Files Names is empty. Only considered for proband.	1. FASTQ 2. VCF	FASTQ
Selected Preset	Optional. Must be the name of a previously defined preset group. The specified preset group appears in the Presets tab for the case. If set to Default, the default preset group is used. If left empty, no preset is applied. See an important note.	1. Free text 2. Default	Exome trio
Storage Provider Id	Conditionally mandatory. Required if Files Names is not empty. Must be from the configured storage provider ID list.	Integer	208
Visualization Files	Optional	Semicolon-separated list of paths to sequence alignment data files of extension .bam, .cram, .tn.bw, .baf.bw, .roh.bed, .lrr.bedgraph, .baf.bedgraph	/giab_project/NA24385.bam

Handling a proband sample with unknown sex

When a sample is user-assigned "Unknown" sex, the system assumes "Female". This affects CNV interpretation on sex chromosomes in case the genetic sex is actually male:

• Chromosome X: CN = 2 is considered reference (REF) for a female genome, so CNVs with two copies are hidden by default. This may cause chromosome X duplications to be missed.
• Chromosome Y: CN = 0 is considered reference (REF) for a female genome, so CNVs with zero copies are hidden by default. This may cause chromosome Y deletions to be missed.

To include these variants in the analysis, enable the Include Reference Homozygosity and No Coverage Calls toggle in Workbench & Pipeline Settings.

Terminology clarification: “Selected Preset” field

Despite its name, the Selected Preset field specifies a preset group used in the case, not an individual preset.

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

Human-readable path for BSSH files in batch CSV

In version 37, we introduced an enhancement to the batch upload process that allows you to provide a human-readable path in their batch CSV for BSSH files.

Validations

When a batch CSV includes a human-readable path, the system performs the following validations for paths in BSSH storage:

1. Single File in the Path:

   • If the provided path contains exactly one file or dataset, the batch upload proceeds successfully.
2. Two Files in the Path:

   • If the path contains two files with the same name (for example, two pairs of fastqs in a dataset) , the system will:

     • Select the dataset marked as QCPassed.
     • Fail the batch upload if both datasets are marked as QCPassed, as this indicates conflicting data.
3. More Than Two Files in the Path:

   • If the path contains more than two files or datasets, the system fails the batch upload, as the path is considered ambiguous or invalid.

Error Scenarios

• Multiple QCPassed Datasets: If two datasets in the same path are marked as QCPassed, the batch upload will fail with a descriptive error indicating the conflict.
• Excessive Files in the Path: If more than two files are found for the provided path, the batch upload will fail, instructing the user to provide a more specific or valid path.

Benefits

• Enables customers to use intuitive, human-readable paths in their workflows.
• Automatically handles dataset selection based on quality control status.