I want to run some sequencing data through the release pipeline that has been analyzed using both the Mutect and Varscan2 variant calling algorithms. Meaning I have two sets of maf files (turned into ssm) on the same donor/sample set, created by the two algorithms. I would like to include the files from both analyses as input to dcc-release, but I'm concerned that doing so would result in some mutations picked up by both algorithms getting counted as two different instances of the same mutation in a single donor.
How have you handled this sort of scenario before? Does the release pipeline account for that sort of input data, or does it expect every instance of a mutation to only appear in the input data once?