Filtering Mutect2 calls post annotation with SnpEff
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
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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.
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.