Can you please provide
a) GATK version used
I believe there is a typo in the commands in sections 1.C and 1.D in the tutorial https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering
The resources arguments are defined incorrectly as
I believe that intsead of a space, there should be a colon after `-resource` and instead of a colon, there should be a space before `hapmap`.
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