If your assay is not yet available in VarSome Clinical, we need you to send us 2 BED files with the coordinates of the targeted regions, one for hg19 and the other one for 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:
- Specify whether it's capture or amplicon-based assay.
- Please send us the corresponding primer location files (bedpe) so that we can ensure that the primers are clipped correctly when analyzing.
- Optional: Specify whether the assay is utilizing UMIs.
In addition, please keep in mind that for variant calling with certain assays corresponding to targeted regions or small gene panels, the variant caller only checks the specific regions or genes defined by the assay or panel. This action is performed by default but can be modified, upon request.