To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Mutect output reproducibility?


I just wanted to ask you that If I run mutect two times with the same parameters, do I expect same output or is there something stochastic going in the algorithm? If yes, I ran mutect with same parameters two time. The only difference was in one file there is vcf output positive and in the other file it was negative.

Thank you very much in advance.




Sign In or Register to comment.