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A possible typo in Mutect2 documentation and a question on filtering results produced by MuTect2 ?
I noticed that in Mutect2's documentation, for creating panel of normals it says "Hapolotype Caller" for -T option. But --artifact_detection_mode did not work with HaplotypeCaller, it only worked with Mutect2. So maybe it should say MuTect2 instead?
Also, is there a quick way to filter the most relevant somatic mutations with MuTect2. This was possible with Mutect when you could just "grep 'KEEP'" to the output and filter possible false positives. Is there a similar way to get the output in that format with MuTect2?