If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
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.
Developing truth sets for VQSR
I am working with macaque WGS and WES data and I'm trying to implement VQSR effectively. In the NHP genomics community there aren't large databases of validated true variant so we're attempting to create our own sets using high quality amplicon and genotyping data that exists within our own lab. My question is how many variants is VQSR expecting to create an effective gaussian mixture model? Do you have any advice as to how to develop a reasonably sized truth set in the absence of databases like dbsnp, hapmap, ect?