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.
Filtering VCF help
I am trying to Filter the VCF based on two filtering criteria, 1) Coverage >3x and 2) Minimum Allele Frequency should be 12% of this >3x filtered Vaiants.
For the filtering based on coverage I used the expression " --filterExpression " DP >= 3", But my question what would be the suitable expression to get my second filtering done ?
Any help will be great.