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.
compare VQSR between two cohorts: same WES different designs
to run VQSR I need to have at least 30 WES... Up to date I used WES data with ~50-60Mb target region (intervals). Now I have 30 new WES ran with a 33Mb target design (CCDS regions). I saw in old posts that there is not a real cut off (minimum number of variants)... and on the other hand if you do not have enough data/variants you will have an error (or warning, I do not remember).
If I want to compare the overall "quality" of the VQSR recalibration between 30 WES with ~50-60Mb design and the same 30 WES previously analyzed (preProcessing/HaplotypeCaller) with the 33Mb desing , how can I do it or what VQSR value/data I need to use? I do not want to compare the vcf files.