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Recommendations for human populations very different from the human reference
I am working on genomes from human populations that are very different (more diverse) from the populations used to build the human reference genome. Thus we are worried about biasing our analyses by relying too much on the reference genome.
In particular, I have a question regarding the indels realigning step (RealignerTargetCreator and IndelRealigner): do you recommend to use the lists of known indels based on the human reference for populations very different from the reference? Or should I run this step without the -known option?