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Somatic Sample Sheet

Upload your somatic cases using a sample sheet

Support avatar
Written by Support
Updated over 7 months ago

A sample sheet is a list that contains information about the samples to be analyzed, including their unique identifiers, clinical data, and other relevant information.

In this article, we will discuss the process of preparing and uploading a somatic sample sheet to Franklin. It is important to ensure that the sample sheet contains accurate and complete information about each sample. This information will be used by the platform to perform the analysis and interpretation of the genetic data. Incomplete or inaccurate information can lead to errors in the analysis and interpretation.

Sample sheet creation

The first step in uploading a sample sheet is to create the file in the correct format. The sample sheet must be a .xlsx file, with each row containing information about a single sample. The columns in the file should correspond to the fields in Franklin.

Fields

Mandatory fields:

  • Case Name - The name that will be given to the case in Franklin

  • Sample Name - The unique identifier of the sample(must be equal to how the sample's files name starts)

  • Cancer Type

  • Assay - What is the assay that should be used for the sample

  • S3 path or baseSpace project and biosample - Where samples files are located on the cloud

Optional Fields:

  • Sex - Male or Female.

  • DOB - date of birth (format MM/dd/yyyy).

  • Batch Name

  • Description

Basespace Upload fields:

  1. Basespace Project - mandatory for DNA-only samples & DNA+RNA samples

  2. Basespace Biosample / Basespace DNA Biosample - mandatory for DNA-only samples & DNA+RNA samples

  3. Basespace RNA Biosample - mandatory for DNA+RNA samples

Supported Flows

Currently, Franklin supports the uploading of somatic sample sheets for:

  • DNA samples: FASTQs, VCF, VCF with BAM

  • Dragen output (Ampliseq, TSO)

Please note that RNA samples require a special configuration. For assistance, please contact your Franklin Account Manager or our Support Team.

Sample Sheet Upload

Once the sample sheet has been prepared, it can be uploaded into Franklin. To upload a sample sheet, users must first log into their Franklin account and navigate to "My Cases", press the "New Case" button and select "Upload Sample Sheet". Select the sample sheet .xlsx file you have prepared and "Next".

Franklin will then validate your sample sheet format. Once the columns validation has been completed, the platform will upload the samples and create new cases for each sample.

Errors and Warnings

Franklin will perform a validation of the sample sheet that has been uploaded and will notify you in case there are issues. In situations the sample sheet is invalid, cases won't be created and an error email with details will be sent to the email address of the user who uploaded the file. In situations the sample sheet has problems but not severe, the cases will be created and a warning email with details will be sent.

Special configurations

In addition to the default configuration of the sample sheet, you can configure your org sample sheet to align it with your organization's preferences. If you wish to make these or other adjustments, please reach out to your Franklin Account Manager or our Support Team.

Examples of Sample Sheets

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