Known Issues with VariantRecalibrator
IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here
IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here
created by bhanuGandham
on 2019-04-09
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.
Updated on 2019-04-09