correct notation of indels/duplication in .vcf file

Question

[User6891]

Hi everyone,

I have to create an artificial .vcf file with SNVs, but also with small insertions, deletions and duplications, that will be used by tools like Exomiser, Extasy, ... for variant prioritization

For SNV's, it's quite easy to fill in the chromosome, genomic position, reference and alternative allele. However for indels & duplication, I'm often not sure how to do this correctly.

If there is a deletion for example, what is then the position that you should put? Position that is deleted, or the base before or after? Same problem for an insertion and a duplication. And which reference allele should you take in those cases? Does anyone know if there are rules to do this?

Answer 1

[Giovanni M Dall'Olio]

Check the VCF format specifications: http://samtools.github.io/hts-specs/VCFv4.2.pdf

In particular, in section 5 contains many examples.