VarSome Clinical offers 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/smal 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. It can be launched from the Launching page analysis or it can be run once the main analysis has finished as a “New CNV subanalysis”: