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Best recommendation for base recalibration on non-human data
I'm currently working on high-coverage non-human data (mammals).
After mapping via BWA, soritng and merging, my pipeline goes like this:
- Remove duplicates via MarkDuplicates.
- IndelRealigner using the
- Fix Mates
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!