Submission of data for EQA

Login

Login to the service takes place via your EQA provider’s portal. Note that an inactive session will end automatically after a while (the exact time-out will depend on the stage).

5 step process to submit EQA results

1. Select submission: On the EMQN/UK NEQAS page you will already have selected germline or somatic. Thereafter, each scheme allows the submission of 3 samples. Once a sample has been submitted, it can still be edited, whereby the old data will be overwritten by the new data. The submitting and editing time frame is up to the closing date specified by the EQA provider.
   
2. Participant practice survey: Provide the information concerning your wet lab and bioinformatics process, including the read depth for variant calls. After completion of the first submission, ensuing submissions allow recall the provided. Go to Next screen.
3. Results submission: Browse and specify the name of the results files that are required by the EQA scheme for assessment (VCF, BED, FASTQ, BAM). File upload starts immediately. The upload is performed in two steps. In the first step the VCF together with the BED files are uploaded. Before progressing to the second step, the participant can still provide a list of genes to include or exclude from the BED file specifications. This additional step is optional, and requires the participant to provide a list of gene names in HGNC format. Note that the option to Skip (as on Figure below) is only available upon re-submission, after a first submission has been completed.
   
   Once the first step is completed, progress to the second step by pressing the Next button. Upload the FASTQ (gzipped) and the BAM files. In order to upload multiple fastq.gz files (e.g. paired end), select all the files during the same browse and pick operation, consecutive uploads will not work. In the file selector dialogue window that opens, you can select multiple files by clicking on them while keeping the Control button pressed. Then, click Open to include all the selected files for upload. Press the Next button to progress after the Processing status display indicates that the upload was successful.
4. Data validation: The system will automatically check the format and consistency of the submitted result files before progressing. If there are errors the process will stop and the user is given feedback on the possible error sources. If this occurs, amended files will need to be submitted. If the reason for failure remains unclear, please contact your EQA provider.
   
5. Confirmation: After validation, press Next to reach the “Confirmation” page, which shows a summary of the data that has been submitted. By then pressing Finish the user is taken to the end of the submission.

!Not sure about formats for files to be submitted? Please refer to the information on standard file formats!