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.
Can HaplotypeCaller be used on drug treated samples?
Hello, I am working on a RNASeq data which consists of liver samples from donors. It is a case-control study where 12 samples are divided as Normal (control) and Rifampin Treated (case). I want to create a sample specific VCF file. I was going through the documentation and I got a bit confused between HaplotypeCaller and Mutect2. Which one should I use to get my VCF file.
In addition, is there a decent way to add gene name, symbol and other annotations to the INFO field of the VCF file?
Any help is much appreciated.