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GATK SNP calling contains all point mutations different from the reference genome. True or false?

I want to knows the difference between SNP and SNV and how GATK source code operate ?

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    To your first question: SNP is what we call a germline single-nucleotide change (because P stands for Polymorphism, a population genetics term) and SNV is what we call a somatic single-nucleotide change (where pop gen terms don't apply, so we use the more neutral V for Variation).

    To your second question: that is a huge question, you're going to need to ask something more specific. Though before you ask, you should read a little bit of our extensive documentation, or at least watch some of the workshop videos.

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