To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

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?

Thank you,



Sign In or Register to comment.