When launching an analysis, you are required to select the assay used to sequence your sample (please see articles Assay missing from the list and Adding an assay to VarSome Clinical if your assay is not listed). If the selected assay is a small panel (i.e. the sample is neither a whole-exome nor a whole genome), VarSome Clinical will perform “targeted calling”. This means that the variant caller is directed to only look at the regions covered by your assay and nothing else.
Even the best sequencing pipeline will produce some off-target reads, reads that align to areas of the genome not included in the assay’s target regions. Searching for variants in these regions will slow down the process of variant finding and will also result in likely uninteresting variants—had you been interested in these regions, you would have used an assay that included them—and incidental findings that a clinician may not even want to be made aware of. We, therefore, use the targeted calling approach to limit the results to the assay’s target regions only.
In order to limit the results to the target region, the variant caller will discard any reads in the alignment bam file that do not overlap with the assay’s regions. If at least one base of a read overlaps with one of the targeted regions, then the read is kept and included in the analysis. If there is no overlap with any of the targeted regions, the read is discarded and not taken into account when calling variants. To ensure that no variants are missed because they fall at the very edges of the target regions, we also include 10bp up and downstream of each region.
The end result of this approach is a faster and more specific analysis.