The gnomAD1 population allele frequency resource is used by Mutect2 to identify variants commonly observed in human populations. These allele frequencies are used to estimate the probability that a candidate variant represents a germline polymorphism rather than a somatic variant.
The specific version in use is distributed by the Broad Institute as part of the GATK Best Practices somatic variant calling resources and can be downloaded here.
The specific dataset used by the pipeline is provided in the following file:
1: Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP, et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020). doi: 10.1038/s41586-020-2308-7