CNV/SV calling analysis

VarSome Clinical currently offers two types of analyses for Structural Variants (SVs) or CNVs depending on the type of input sample.

Whole exome sequencing (WES) or targeted panel data

For such samples, we use the ExomeDepth CNV caller. The tool requires five or more (ideally between five and ten) non-WGS germline or tumor samples that have already been analyzed on VarSome Clinical. These will be run as a cohort with each sample analyzed using the rest as a control. The samples should all have been sequenced using the same assay since CNV calls will only be made in the assay's target regions. For optimal results, the selected samples should:

  • be from the same sequencing run
  • come from individuals unrelated to each other and
  • be of the same sex (either all male or all female) if looking for CNVs on chromosome X. If  the samples are not all of the same sex, calls on the X chromosome will not be reliable.

All samples will be analyzed together and the results (along with a new visual display) of each sample will be shown as a sub-analysis of that sample. 

Please note that an inherent limitation of WES is that it produces reads only covering the ~2% of the human genome that falls in exons. Therefore, the full spectrum of CNVs and breakpoints may not be completely characterized. In addition, many large CNVs and cross-chromosome events may not be detected. For optimal results, we suggest either sequencing the entire genome (WGS), or a different experimental approach such as array CGH. Nevertheless, CNV detection based on WES data may give a quick insight into CNV patterns for a specific disease or phenotype. For more details on the limitations of calling CNVs in such data, please see [1].

Whole genome sequencing (WGS) data

For WGS samples, we use delly an integrated structural variant (SV) caller tool that can detect both CNVs and other forms of Structural Variants (SVs) at single-nucleotide resolution in short-read genomic sequencing data. It combines 3 different approaches (paired-ends, split-reads and read-depth) to discover extensive genomic rearrangements.

For WGS samples, VarSome Clinical offers:

      1. Germline SV calling: Call SVs on a single germine WGS sample.One or more whole genome (WGS) samples, each run as a separate analysis. 
      2. Somatic SV calling: One tumor sample and a matched control (one tumor and one germline) whole genome (WGS) samples, from the same assay, to be run as a Tumour/Normal analysis. 

Sample selection

You can assign a unique “tag” to each already run full sample:

Apply a tag

Alternatively, you can associate a tag when you launch an analysis from FASTQ:

Setting up FASTQ analysis

And finally, type in the tag to select samples for a CNV/SV analysis:

Setting up a CNV/SV analysis

CNV annotation starting from VCF

VarSome Clinical doesn't currently annotate CNVs in user-submitted VCF files, it only annotates CNVs that are the result of VarSome Clinical's own CNV-calling pipeline, starting from FASTQ. 

A step-by-step example on how to run a CNV/SV analysis

Select “CNV/SV analysis” from the “Launch analysis” drop-down menu on VarSome Clinical:

If using exome or targeted panel data, the VarSome Clinical interface allows you to select a minimum of 5 and a maximum of 25 already analyzed samples to be used as a cohort for CNV calling. For best results, we recommend you select 5-10 samples from unrelated individuals of the same sex that were sequenced on the same sequencing run.


Each sample’s results will appear as a sub-analysis of the main analysis.

CNV subanalysis

If using WGS data, you can choose either:

  1. One or more WGS germline sample(s). Unlike for WES and targeted data, these will each be analyzed separately. You can simply launch more than one at once for convenience.
  2. A Tumor/Normal comparison analysis of one tumor and one germline WGS sample from the same individual.

    See also


    [1] R. Tan et al., An Evaluation of Copy Number Variation Detection Tools from Whole-Exome Sequencing Data, Hum. Mut.,2014