Validation of VCF files

Both VarSome Pro as well as VarSome Clinical accept any VCF file, however it must conform to the standards for VCF files.

The issue is usually a malformed header or a missing header.

You may use one these validators:

Basically, the VCF file needs to follow the VCF standard correctly. Another quick test is to just see if a standard program like bcftools (https://samtools.github.io/bcftools/bcftools.html) recognizes the file and doesn't complain.

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.