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Mutect output reproducibility?

morovatuncmorovatunc turkeyMember

Hi,

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.

Tunc.

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