This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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?