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 VCFs that contain 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 mixed VCF file to run as a sub-analysis for an already analyzed sample.