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
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
Comment