The syntax for specifying argument tags has changed (and the documentation was out of sync for a while, though it is now fixed). The tags must now be specified with the argument name, not with the argument value, like this:
--resource:hapmap,known=false,training=true,truth=true,prior=15.0 /trainee/ref/hapmap_3.3.hg38.vcf
Note that the ":" and tags are listed with the argument name ("-resource"), not with the file name.
1 comment
Looks like this update has not made it through to https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering
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