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Does it hurt to run the "data pre-processing for variant discovery" on "analysis-ready" bam files?
This might be a very naive question, but I would like to confirm.
So I have some bam files from a collaborator (who got those files from Broad Institute, I believe) but I do not know whether they are "analysis-ready" or not (probably yes?). Is there a reliable way to check whether those BAM files are "analysis-ready" or not?
To be safe, I'm running the "Best Practice" Data pre-processing for variant discovery on those files. So if they are analysis-ready, it shouldn't hurt, right? Thank you!