Hi GATK Users,

Happy Thanksgiving!
Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!

GATK Staff

Functionality request

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.

Best Answer


Sign In or Register to comment.