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 on exome of small specific population
I've asked this question at the workshop in Brussels, and I would like to post it here:
I'm working on an exome analysis on trio. I would like to run VQSR of filteration on the data. since this is an exome project, there are not a lot of varients, and therefore, as I understand. the VQSR is not accurate. You suggest to add more data from 1000Genomes or other published data.
The families that I'm working on belongs to a very small and specific population, and I'm afraid that adding published data will add a lot of noise.
What do you think, should I add more published data? change parameters such as maxGaussians? do hard filteration?