Hello, I'm trying to figure out the Pipeline for Annotating Mutations and Filtering Putative Germline SNPs that is described in the data guide and I am having an issue the non-TCGA subset VCF of ExAC 0.3.1. At the last step of the pipeline, there is a filtering step by the gnomAD allele frequency (AF) column. Looking at the vcf file from gnomAD, there is no such column (the info lines reveal the VEP was run to create that file without the gnomAD option). When you processed the GENIE files, did the raw exac.non-tcga VCF already contained gnomadAF data or if they added them in during processing? Thank you, Maayan.

Created by maayanbaron
Hello @maayanbaron, The non-TCGA subset VCF of ExAC 0.3.1 pipeline was performed on earlier releases. In the most recent GENIE releases, the data files get re-annotated by [Genome Nexus](https://docs.genomenexus.org/) during processing. We are looking into revising the data guide to account for any updates in annotation and filtering pipelines for the most recent releases. Please let us know if you have any more questions. Best, Chelsea
Hi @maayanbaron, Thanks for your interest in the GENIE data - we will respond soon with an answer.

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