Mutect --genotype-germline-sites status
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e) Will Mutect2's --genotype-germline-sites be in future releases?
I notice that this flag is still set to `EXPERIMENTAL` in the Mutect2 docs. Is there a way I can track the status of this feature? It is important for the functionality of the pipeline I have built (i.e. we want to be able to see all of the germline variants that Mutect wants to call -- doesn't have to perfect per sé, but those calls are important), so we want to ensure it stays in the picture because it seems to be working for our needs (even after a lot of pressure testing).
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Hi Alijah O'Connor,
The --genotype-germline-sites feature is no longer in an experimental status, it's just an oversight on our part that it is still marked that way. It's definitely an advanced option but it will not disappear.
I have created a github ticket so that we change this in our documentation: https://github.com/broadinstitute/gatk/issues/7318. Thanks for bringing this to our attention!
Best,
Genevieve
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Genevieve, this is great news, thank you!
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