Known Issues with VariantRecalibrator
Solutions to Problems | Created 2019-04-09 | Last updated 2019-04-09

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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.

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