Annotate variants for cancer genomics studies

Question

[epigene]

I'm relatively new to analyzing variants data generated by WES in a cohort of cancer patients. I've called variants using Mutect2, annotated them with VEP and now I want to annotate these variants with information such as whether they are known variants in dbSNP and their pathogenicity prediction, whether it's known in ExAC etc.

What tool is the best for doing this type of annotation and also being actively maintained that handles both hg19 and hg38 genome build for cancer genomics? Thanks!!

[brunobsouzaa]

If you are using VEP as command Line, you can use Plugins such as dbSNP, dbNSFP (with proper values) and Clinvar. Also, you can add gnomAD annotations. You can also check your variants in oncoKB to see if it's actionable and has a drug-related treatment. But, you'll have to do this manually or purchase a license to use oncoKB annotator! COSMIC is also a great catalog.

[epigene]

Yes, I want to add these kinda annotations, the question is that is there a tool that can take all these databases and integrate them on VCF?

[brunobsouzaa]

Yes, you can put almost all of them in your VCF using VEP command line. The only one that is not possible is oncoKB. Take a look into VEP documentation. You can output your results file as VCF or tab delimited file.