Can you please provide
a) GATK version used v126.96.36.199
b) Exact GATK commands used
c) The entire error log if applicable.
I am using GATK v188.8.131.52 and I am interested in running Mutect2 with an alleles file (force-call-alleles.vcf). In the example on the web site which shows an example of the use of the --alleles parameter, it states that the force-calls mode calls alleles in the force-call-alleles.vcf in addition to any other variants Mutect2 discovers. Is it possible, however, to restrict the output to variants ONLY present within the force-call-alleles.vcf file?
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