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error in Mutect2 when using dbsnp?

etcetc Member
edited February 16 in Ask the GATK team

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 (
I am using the GATK docker image with GATK version

gatk-4.beta.5 (local) jar accepts the --dbsnp option as valid.
Please advise.

Best Answer


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