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 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.
For family cases, each line will include a single sample, the case name will be the same for all family members and the field relationship will be used to describe the family structure. Besides the family case, single analyses will be created for each family member.
Fields
Mandatory fields:
case name - The name that will be given to the case in Franklin
We recommend using a similar or identical name to the sample name provided. In family cases, all family members should have the same case name (but different sample names).
s3 path / baseSpace project - Where samples files are located on the cloud
sample name - The unique identifier of the sample:
Use a sample name that matches the prefix used in the sample files' names. For example, if your file is named 'Sample001_data_etc.fastq', enter 'Sample001' as the sample name.
baseSpace biosample - The name of the sample on base space
assay - What is the assay that should be used for the sample
relationship - Mandatory for family cases, if empty then the sample is considered as the proband. In a family case, only one sample can be set as the proband.
Optional Fields:
Sex - Male or Female.
dob - date of birth.
phenotypes - HPO terms, separated by semicolon.
affected - Whether the sample is affected or not. values are yes/no. If the cell is empty it is considered not affected
ethnicity
labels
description
hard panels - 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 panel list) in which areas variants will be annotated and presented in the case. Genes should be separated by semicolons.
Soft panels - 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.
Batch name
Custom fields - All custom case fields of your organization can be used as fields in the sample sheet.
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 account manager in Franklin or our support team.
For example, you can define:
Whether to process a partially valid sample sheet
The number of files that are required for case files to start the pipeline (for each case type)
Whether to create single cases for samples in the family analysis