Filtering Mutect2 calls post annotation with SnpEff

Question

[philomath_physicus]

Hello,

I have a query about filtering Mutect2 somatic calls that have been annotated using SnpEff. Can I filter the calls in accordance with the recommended best practices, i.e. blacklist/filter calls with DBSNP, Panel of Normals? Will the annotations be valid afterwards?

Thank you for your input! ~Philomath

[jared.andrews07]

What do you mean will the annotations be valid? Removing variants in dbSNP or also called in a panel of normals will not change the annotations of those remaining.

[ATpoint]

Are you sure that you want to categorically remove dbSNP variants? What do you gain by this filtering step? Unlike most people think, dbSNP does contain disease-associated variants. The idea of removing dbSNP variants in order to exclude common variation is false (correct me if I am wrong here). Rather, filter your variants against the 1000 Genomes project (e.g. using Ensemble Variant Effector Predictor, VEP) to exclude common variation.