Resource Annotation by Variant rather than Site

mdjones

I would like to have certain annotations applied only if the variants in the resource and the target have the same genomic change. Ex: In Cosmic the following variants are present.

12      25398284        .       C       G       .       PASS    Genename=KRAS;MutationAA=p.G12A;MutationCDS=c.35G>C
12      25398284        .       C       A       .       PASS    Genename=KRAS;MutationAA=p.G12V;MutationCDS=c.35G>T
12      25398284        .       C       T       .       PASS    Genename=KRAS;MutationAA=p.G12D;MutationCDS=c.35G>A

However, in my VCF file I get the G12A annotation for all variants at this site even if the actual change is G12V or G12D.

Is this possible?

Geraldine_VdAuwera

Unfortunately that is not currently possible with the GATK, sorry.

mdjones

Thanks Geraldine. Now I am wondering if I should learn how to write GATK walkers or just use my own code to create a Variant Change aware VariantAnnotator.

Geraldine_VdAuwera

If it was me I would probably choose to create an annotator based on existing VariantAnnotator modules. If you do decide to implement this, we'd be happy to look at your code and consider adding it to the toolkit.