I am running Mutect2 with various options. Most options are running as expected, but when using the --dbsnp version I am now seeing an error:
A USER ERROR has occurred: dbsnp is not a recognized option
In the resulting error log, --dbsnp does not appear among the list of recognized arguments. In the online tool documentation, however, it is listed as a valid option (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php#--dbsnp)
I am using the GATK docker image with GATK version 4.0.1.2
gatk-4.beta.5 (local) jar accepts the --dbsnp option as valid.
Please advise.
