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
use existing sample - to create tumor cases from samples that already exist in Franklin, add a column named "use existing sample". Fill “yes” only for the samples (rows) of interest. For the remaining samples, fill "no" or simply leave the column empty. Following upload, new cases will be generated seamlessly. This functionality does not affect existing cases that contain the samples of interest.
hard panels - knowledge base (KB) panel names that will define the areas in which variants are annotated and presented in the case. Panels should be separated by semicolons.
For more details about hard panels see this article.hard panels single genes - A list of gene names that will define (together with the hard panels list) in which areas variants will be annotated and presented in the case. Genes should be separated by semicolons.
Soft panels - knowledge base (KB) panels that will be added to the case and will allow to easily filter variants according to the list of genes. Those panels, unlike hard panels, can be removed during the analysis process.
Basespace Upload Fields:
Basespace Project - mandatory for DNA-only samples & DNA+RNA samples
Basespace Biosample / Basespace DNA Biosample - mandatory for DNA-only samples & DNA+RNA samples
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.
Sample sheet troubleshooting and support
If you encounter login issues please refer to the Troubleshooting article
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.