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Hi all!

I'm currently working on high-coverage non-human data (mammals).

After mapping via BWA, soritng and merging, my pipeline goes like this:

  1. Remove duplicates via MarkDuplicates.
  2. RealignerTargetCreator
  3. IndelRealigner using the --consensusDeterminationModel USE_SW flag
  4. 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!

Sagi