Adding an assay to VarSome Clinical

Learn how to upload your custom BED file.

VarSome Clinical customers

If you are a VarSome Clinical customer and your assay is not yet available in VarSome Clinical, we can add your assay if it is an assay we can support.


If you need us to add a new assay, the first question is whether this is a standard assay or if it requires special handling. Examples of special handling include but are not limited to assays with Unique Molecular Identifiers (UMIs), assays that are designed to produce mixed RNA and DNA sequencing data, assays targeting specific classes of variants such as certain large deletions in genes like CFTR and various other special cases. If you do not know if an assay requires any special treatment, please talk to your assay providers and ask them if any special bioinformatics approaches are required to handle the data the assay will be used to generate.

Assuming no special handling is required, we will need you to send us 2 BED files with the coordinates of the targeted regions, one for each version of the reference genome (hg19 or hg38). If you send only one, the platform will allow the selection of the reference genome in line with the reference genome used for that BED file.

In addition to that we need you to:

  1. Specify whether it's a capture or amplicon-based assay.
  2. In case it is an amplicon kit, please send us the corresponding primer location files (in bedpe format) so that we can ensure that the primers are clipped correctly when analyzing.
  3. Specify whether the assay uses UMIs, at which point we will need to ascertain if it is using one of the UMI systems that Varsome Clinical supports. Please contact us if you need more information. 

Please keep in mind that for assays targeting relatively small regions of the genome (i.e. assays that are neither whole-exome nor whole genome) variant calling will be performed in targeted mode, only looking at the regions mentioned in the assay.

Prospects evaluating VarSome Clinical during the free trial period

Unfortunately, we cannot add assays for free trial users. However, this should not be a problem. If your assay is not listed, simply choose one of the two "generic" options:

  • either “Generic capture kit” or
  • “Generic amplicon kit”.
Assay selection when launching a new analysis

This option must be in line with the chemistry of your sequencing assay, because this affects how we handle PCR duplicates. Visit Sequencing Assay Selection for more information. And so, make sure to select "Generic amplicon" if your actual assay is an amplicon kit and "Generic capture" if your assay is a capture kit.

As long as you choose the right chemistry type as described above, the results will be the same as if we had added your assay. The only differences will be that we will not give you statistics about the percentage of reads that fall on target and we will not run the variant calling in targeted mode  (since we do not know the targets) so you may see variants that fall outside your regions of interest. However, the results will be correct and reliable.

If you finally decide to join us and become a VarSome Clinical customer, we will be happy to add your assay to our platform, as described above.