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 - overlapping training sets
when I have multiple training sets for VQSR,
what happens with overlapping variants between these two sets?
Especially when the two sets have different priors attached.
Example from Best Practices:
I have HapMap with prior Q15 and
1000G with prior Q10.
How will a variant influence the model when being in both sets?
I would expect that only the highest prior will be used.