The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
error in Mutect2 when using dbsnp?
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 126.96.36.199
gatk-4.beta.5 (local) jar accepts the --dbsnp option as valid.