We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

What are the parameters used by GATK to define a SNP?

I'm a master student and I'm using GATK, for the first time, to find SNP in RNAseq data. I would like to know what GATK considers a SNP. What are the parameters used for this, such as: frequency and number of reads aligned at the position of SNP.



Sign In or Register to comment.