Setting up CNV/SV analysis

You may start a CNV/SV analysis from:

  • 5 or more (ideally, 10) non-WGS germline or tumor samples, from the same sequencing run, as a cohort analysis
  • 1 or more whole genome sample as separate analyses
  • 1 germline and 1 tumor whole genome samples, from the same capture kit, as a Tumor/Normal analysis

How to select samples for CNV/SV analysis?

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

Apply a tag

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

Setting up FASTQ analysis

And finally, that 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. Also, VarSome Clinical requires that all lines in a VCF file be specific variants; we don't support the "NON_REF" lines.