mutect2 is very stringent about sorting and will crash when intersecting a chromosome with a bed file. even if there is nothing that would let you know that. so will have to add reference sorting (and possibly removing the chrM, MT from the bed file) when doing a scatter gather of Mutect2 along with all of the other standard dynamic fixing of bed files...it's always something. It's possible that you can get around this by making picard interval bed file and using that instead, so I might try that since that is made and pass that through when I make an actual pipeline.
mutect2 is very stringent about sorting and will crash when intersecting a chromosome with a bed file. even if there is nothing that would let you know that. so will have to add reference sorting (and possibly removing the chrM, MT from the bed file) when doing a scatter gather of Mutect2 along with all of the other standard dynamic fixing of bed files...it's always something. It's possible that you can get around this by making picard interval bed file and using that instead, so I might try that since that is made and pass that through when I make an actual pipeline.