CSV format requirements for variant upload

General CSV format requirements

A CSV file used for variant upload to Curate must meet the following requirements:

• File extension: .csv.

• The first row contains column headers.

• Each column represents a data field.

• Column headers are case-sensitive and exactly match this specification or a template.

• Each row after the header represents a variant.

• There are no empty rows between the header row and variant rows and between variant rows.

• Maximum file size: 10 MB.

• Maximum number of variants: 5000.

• Supported variant types:

  • SNV (SNV, indel)

  • CNV (DEL, DUP)

• SNV and CNV rows may be included in the same file if all mandatory fields are present (see Field summary).

CSV file templates

You can use the templates below as a starting point.

2KB

variants_batch_template_GRCh37.csv

Open

2KB

variants_batch_template_GRCh38.csv

Open

Field summary

Field (column name)	SNV	CNV
Vartype	Mandatory	Mandatory
Chromosome	Mandatory	Mandatory
Position	Mandatory	Mandatory
REF	Mandatory	Mandatory
ALT	Mandatory	N/A
End	N/A	Mandatory
Overlap	N/A	Optional
Pathogenicity	Optional	Optional
Disease	Optional	Optional
Interpretation	Optional	Optional
Notes	Optional	Optional
Transcript	Optional	N/A

Access-controlled fields

Some fields require specific user permissions to update.

Access-controlled fields include:

• Pathogenicity

• Disease

• Interpretation

• Notes

• Transcript

If you do not have permission to update a field:

• Curate ignores the field

• The variant is still created

• The upload summary in the last step of multiple variant upload marks the variant as Partial Success and lists the ignored fields \

Batch variant CSV file validation rules

Only fields listed on this page are processed. Any unsupported fields included in the CSV file are ignored.

See the tables below for fields supported for each variant type: mandatory (in red font) and optional.

Single nucleotide variants

The fields for an SNV variant should be filled in according to the rules in the table.

Table 1. Validation rules for SNV fields

Field (column) name	Field details	Expected input	Example
Vartype	Mandatory.	SNV. Applicable for both SNV and indel.	SNV
Chromosome	Mandatory.	1 - 22, X, Y, M	3
Position	Mandatory.	Integer	123000
REF	Mandatory.	A, T, G, C, or a string of these letters	G
ALT	Mandatory.	A, T, G, C, or a string of these letters	GACT
Pathogenicity	Optional. Access-controlled.	Pathogenic, Likely pathogenic, VUS, Likely benign, Benign	Likely pathogenic
Disease	Optional. OMIM ID.	Integer	113705
Interpretation	Optional. Access-controlled.	Free text under 65000 characters	Free text
Notes	Optional. Access-controlled.	Free text under 65000 characters	Free text
Transcript	Optional. Access-controlled. NCBI RefSeq transcript ID.	NCBI RefSeq transcript ID	NM_000183.3

Copy number variants

The fields for a CNV variant should be filled in according to the rules in the table.

Table 2. Validation rules for CNV fields

Field (column) name	Field details	Expected input	Example
Vartype	Mandatory.	DEL, DUP	DEL
Chromosome	Mandatory.	Integer	3
Position	Mandatory.	Integer	123000
End	Mandatory.	Integer greater than Position	124000
REF	Mandatory.	A, T, G, C	G
Overlap	Optional: if absent or empty, the fallback value 70 is assigned.	Integer 0-100	80
Pathogenicity	Optional. Access-controlled.	Pathogenic, Likely pathogenic, VUS, Likely benign, Benign	Likely pathogenic
Disease	Optional. Access-controlled. OMIM ID.	Integer	113705
Interpretation	Optional. Access-controlled.	Free text under 65000 characters	Free text
Notes	Optional. Access-controlled.	Free text under 65000 characters	Free text