correct notation of indels/duplication in .vcf file
1
1
Entering edit mode
7.6 years ago
User6891 ▴ 310

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?

vcf duplications indels • 7.0k views
ADD COMMENT
3
Entering edit mode
7.6 years ago

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

In particular, in section 5 contains many examples.

ADD COMMENT

Login before adding your answer.

Traffic: 2127 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6