How to add custom annotation to a vcf ?

[swNGS]

Hi,

I have what I hope is a fairly simple question....

Suppose I have a vcf file (lets call it vcf1). This is a list of variants created by GATK from a targeted resequencing project from a list of genes.

I am interested in annotating this vcf with information from a customised reference file (call it vcf2). An example might be a list of in-house known pathogenic mutations that we have previously seen.

How should I go about doing that?

I have previously used Annovar's pre-built reference vcfs to annotate with functional info & gene name, transcript etc, but dont know how to go about creating a reference lookup myself, and then applying it to lookup a per-sample vcf. Should I be referencing a genomic locus, or relative to a specific place in a transcript ?

Any pointers would be much appreciated

Chris

[SeekAnswers]

I think the genome locus (chromsome and location within the chromosome) should be fine as a reference key.

[swNGS]

Does anyone have any suggestions how to to about this?

While this is an intermediate goal, what I am hoping to achieve in the long run is to warehouse all variants seen from the same multi-gene assay and be able to annotate new samples being run on the same assay with allele frequency data, or pathogenicity info that we may have stored for variants previously seen