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MuTect2 PON CombineVariants
In the MuTect2 documentation, it says:
"For full PON creation, call each of your normals separately in artifact detection mode. Then use CombineVariants to output only sites where a variant was seen in at least two samples"
However, if you only have two samples in your panel, then filtering by two is going to create a lot of false negatives. On the other hand, if you have 1000 samples, two may not be enough. Do you really mean always use two samples, or should that be a fraction of total samples?