Assay missing in the list

Learn why your assay/kit might not be listed when starting an analysis from FASTQ.

VarSome Clinical is capable of processing any NGS data from targeted DNA or whole exome/genome sequencing, be it a commercial or custom gene panel, exome or genome, as long as the data is produced on an Illumina sequencer. 

When launching an analysis starting from FASTQ you need to select the Assay. Assay details will be used to calculate the coverage of the target regions included in the kit, and to calculate quality control metrics. In the list you can see number of assays already supported by VarSome Clinical. There are several possibilities why your assay is not available in the list:

1) VarSome Clinical use is limited to a certain assay only

In certain cases, VarSome Clinical comes bundled with the assay directly from the assay manufacturer or your distributor (i.e. bundled solution), as is the case of Swift Biosciences gene panels, for example.

Although the platform use might be initially restricted to a particular assay only, in principle there is nothing to stop you from using it for other NGS data. Simply, get in touch with us and let us know what kind of NGS data you want to analyze with VarSome Clinical.

2) All vs. Favorite assays

As VarSome Clinical can process any kind of NGS data, the list of Assay is very long. To eliminate the need to scroll through the long list of Assay whenever you are launching an analysis, you can simply mark certain assays as favorite. Remember to check your settings for favorite assays.

3) Your assay is not yet available on VarSome Clinical

In the case of a custom panel or in the case your assay is not yet supported, we need you to send us a BED file with the coordinates of the targeted regions. Also, send us the corresponding primer location files (bedpe) so that we can ensure that the primers are clipped correctly when analyzing. In addition to that, answer please these two questions:
  1. Is this a capture kit or an amplicon kit?
  2. What is the reference genome, hg19 or hg38?