IS GC score same as Call rate?
Hi guys, Is GC score same as Call rate? If not then what is GC score and what is Call rate? Thank you in advance
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I think this article will be really helpful to you - your past questions have been severely lacking in detail as well, and that needs to be addressed if you are to ask for help successfully. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202