Is there a minimum length of CNVs that can be detected by the CNV calling pipeline ?

(applies to WES and panels)

There is no specific minimum size of CNV that can be detected by VarSome Clinical. The length of CNV calls depends on the length of the target genomic intervals of the assay used to sequence the sample. Such intervals are encoded in the form of a .bed file and are assay specific. In whole-exome sequencing (WES) assays, typically each interval is an exon, however assays may also target additional, much shorter regions that are a few bases long. In gene panel assays, the length of regions also varies.

VarSome Clinical's CNV calling pipeline is read depth based, so higher read counts generate more robust CNV signals. On the other hand, low read counts may result in untrustworthy calls. VarSome Clinical checks the coverage and informs the user if it is too low in the call region (Call Quality column). User can also visually inspect the relevant region using the provided  links to IGV/JBrowse. Detailed sample coverage analysis is available in the Coverage Report (available in the Analysis Actions menu).