In using "CountCovariates" for base quality score recalibration, I got a complaint that the platform information was missing. I can force it to default to "illumina" with the "-dP" option, but that doesn't seem wise, and I imagine that more problems will crop up in the future if I do that. I looked in the bwa manual to see if there was an option in sampe (like I've seen for adding read group information), but I didn't see anything. Does anyone know how to add this information?
Thank you.
Eric
Thank you.
Eric
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