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.
VQSR / CNN filtering for small (~100) gene panels
I'm trying to perform germline variant calling on a panel with ~100 genes. I was wondering what the bare minimum (in terms of sample size) would be for variant filtering via VQSR. If the sample size is prohibitively high given the size of the gene panel, would it be appropriate to pad the training set with exome data from 1000G or ExAC? In general, is there a minimum number of variants needed to train the model?
Also, is there a timeframe for the official release of GATK CNN, and would something like this be applicable to my gene panel once available?
Thanks for your help!