CNV/SV annotation (from VCF)

VarSome Clinical provides a pipeline to annotate CNVs from VCF files. There are two ways to annotate CNVs from VCFs.

  • Provide a valid VCF file that contains both copy-number-variants (CNVs) and SNPs/small INDELs (mixed file) when launching a new analysis either from FASTQ or VCF. Files that include both small variants and CNVs will be split to two separate files, one for small variants and one for CNVs (i.e .filtered and .cnv).  
  • Provide a valid VCF file containing only CNV variants.

The CNV analysis from VCF is launched as a sub-analysis of the main analysis. You can launch a CNV annotation by:
- Adding a CNV VCF file when defining your sample. 

- Launching the analysis once the main analysis has finished as a "New CNV sub-analysis" either from single or multi sample analyses. 


From the Dashboard menu:

From the Analyses menu: