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I wonder whether it's possible to have a parameter to suppress the commandline from the output of SelectVariants and VariantFiltration? If I use JEXLs in these functions, and if those JEXLs have double quotes in them, VCF output would break for obvious reasons. So, let's say, if I use SelectVariants, I'd have to use something like the following for downstream compatibility:
-select "vc.getGenotype('TUMOR').getAD().0 >= 5"
But since there're nested quotes here, this would make writing shell scripts a hassle, since the JEXL would need to be hard-coded into the java invocation.