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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.