It is said on the GATK web that Mutect2 is a BETA tool and is not yet ready for use in production. But I actually found some paper has already used it. So can Mutect2 be used in paper practically?
Sure, papers using mutect2 appear all the time. An official publication is not required to use a tool productively, see bwa mem arguably the most prominent alignment software in bioinformatics has no official publication in a peer-reviewed journal.
Since gatk 4.1.0.0 mutect2 is not in beta anymore : https://github.com/broadinstitute/gatk/releases
So you can use it in paper without problem ;-)
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version 2.3.6
Make sense. I think I have mistaken productive use for paper use. Thank you for your answer!