Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Expected number of variants in WES data
I'm interested to know the approximate number of high quality variants reported in WES data. According to this page on the GATK site - https://software.broadinstitute.org/gatk/documentation/article?id=6308 , this is about 41k. However I observe only about 30 - 32k variants in exome data for CDS regions (Gencode v19). I see similar numbers when I analyzed the 1000 genomes phase 3 calls. I'm not sure why the numbers I get are lower. Any information about the reference for those numbers and what region was used and ranges usually observed would be helpful.