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.
Truth & Control sources- HapMap and 1000G
I apologize in advance if this question seems like a stupid one, but I have always thought that sources such as HapMap and 1000G from the resource bundle that we use in VQSR are comprised of many global samples, but when I peaked inside of the vcfs, I only saw a reference and alternate allele for seemingly 1 sample only. What am I missing here?
If the multisample genotype info is somehow Incorporated into the vcf index file then is there a way to display the contents of the index file so that I can remove all African samples since they are totally irrelevant to my test sample and seem to be negatively affecting The calibration and the calls for my test sample