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Any recommended changes to Best Practices for genotyping-by-sequencing data?

mcrossleymcrossley Madison, WIMember

Hi, I saw a similar question to mine was posted a few years ago but didn't see an answer there.
I am specifically wondering about the pre-processing recommendations - like how duplicate mapping would affect genotyping-by-sequencing data.
Would it be okay for me to skip ahead to variant calling?
Thanks for any insight you can give,
-Mike

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