I'm currently working on high-coverage non-human data (mammals).
After mapping via BWA, soritng and merging, my pipeline goes like this:
I currently want to begin the recalibration step before doing the actual variant calls via UnifiedGenotyper.
Since I'm working on non-human data, there is no thorough database I can trust as an input vcf file for the recalibration step.
What is your recommendation for this for non-human data?
Thank you very much!