11. Storage Management

This document describes how to monitor the storage space and how to possibly reduce it.

Storage fees are calculated at the end of each month, based on the volume of data that has been uploaded into VarSome Clinical in order to run analyses. They reflect the storage costs of Saphetor data centers or the storage costs charged by 3rd parties (like GCP - Google Cloud Platform) to Saphetor.

If a new sample has been uploaded during a given month, the storage costs for that month will be prorated based on the day of the upload.

Saphetor is not responsible for monitoring or managing the storage costs of any customer. This should be done by each end customer, possibly in coordination with the local distributor.

Monitoring the storage space

In order to check the volume of data that will be charged, each Account Administrator can visit
sso.varsome.com (using his/her institutional user email address) and click on the Billing menu:

This window contains the monthly storage reports, in pdf and xls format, as well as the most
recent billing entries, invoices history and account statements. The account administrator can
then either filter on specific files or choose from the list.

Managing the storage space

There are 5 different options to possibly limit the volume, and hence the related costs, of
samples data storage:

  1. Keep all the data
    1. The Storage Fee applies to all the data available in the client’s account. This is the
    2. default option and needs no user action to be applied.
  2. Remove FASTQ; keep the BAM and results.
    1. Space occupied is lower than option 1 by approximately 25%.
  3. Remove BAM; keep the FASTQ and results.
    1. Space occupied is lower than option 1 by approximately 50%.
  4. Remove all the raw data (FASTQ and/or BAM); keep the results only.
    1. Space occupied is approximately 75% lower than option 1, as the annotation data
    2. doesn’t take up much space.
  5. Archive the sample.
    1. No Storage Fee applies.
    2. Samples results/annotations are not available for browsing in VarSome Clinical.
    3. The archived sample is still cross-referenced with other samples and sample links are still shown in the tab with cross-referenced samples, along with the patient's phenotypes.
    4. Custom Variant Classifications set up initially for the archived sample will stay available when browsing other active analyses. The phenotypes assigned to the archived sample
    5. are still available in the sample information.
    6. All sample data are deleted and not available anymore. Only the VCF file is stored for possible sample re-annotation when unarchiving the sample.
    7. The client may unarchive the sample. When doing so, the re-annotation fees will apply. For more details, please contact sales@varsome.com.
    8. When un-archiving the sample, VarSome Clinical will annotate the sample (VCF file) against the latest annotation data, which may cause annotation and classification differences between the original sample and the unarchived sample. 

Setting up VarSome Clinical storage preferences

The storage preferences within VarSome Clinical can be modified in order to define for how long
the user wants to store the FASTQ and BAM files and when they want their analyses to be

In the VarSome Clinical platform, hover over your username on the right top of the window, then
select "Preferences":

Only the group supervisor (one by account) will have permission to modify these preferences.
If you do not have a group supervisor yet, please contact support@varsome.com and let them
know who should be your group supervisor. Once the group supervisor has access to the "Preferences" menu, they will be able to set up the storage preferences for each type of file:

This shows the time periods from the day of the analysis.

WARNING: Please, bear in mind that updating the storage preferences might lead to the imminent deletion of data. For example, if you select to keep FASTQ and BAM/BAI files for one year, all the FASTQ and BAM/BAI files of samples analyzed more than a year ago will be removed. If BAM/BAI files are deleted, certain functionality that depends on the presence of those files will not be available any more e.g. (JBROWSE/IGV) read alignments visualization.

A warning will be displayed in VarSome Clinical when updating your preferences.

Deleting / archiving data

Within VarSome Clinical it is also possible to immediately delete some FASTQ and BAM files, or
also archive some analyses, without waiting for the time period defined previously.

For each single sample analysis that was launched from a FASTQ file, the user can click on the
three horizontal bars on the right side of the sample name. They will then find the following