Agilent's OneSeq is based on the target enrichment of small regions spread through the whole genome in ~10kb spaces between them. It allows detecting down to 300kb long CNVs in the sample genomes. The panel is similar to exon panels, however instead of exons it usually covers intergenic regions.
Thus, you can use VarSome Clinical's pipeline for CNV for analyzing the data if enough samples are sequenced in one sequencing run, using batch reference - the very same strategy as for exon panels.
Agilent SureCall
There is a free Agilent tool called SureCall specifically designed for OneSeq data. It uses a separate reference sample (provided as DNA sample by Agilent) in contrast to VarSome Clinical's pipeline for CNVs.
SureCall uses B-allel frequency analysis. There is a trick for detection of LOH using a reference sample as you can then detect different haplotypes in the aberrant regions and therefore determine this balance translocation.
However, number of our clients uses VarSome Clinical's CNV pipeline for OneSeq data (with batch reference) and are more than satisfied with the results.