I am wondering if there is an updated version of the RNA Mutect pipleline besides what is detailed on the following github page: https://github.com/broadinstitute/RNA_MUTECT_1.0-1 . I have been following the Mutect2 pipeline and am developing a PoN, but am wondering what I should use for the interval list, since this is RNA-based. Currently, I am getting stuck on the GenomicsDBImport command, receiving this error:
what(): GenomicsDBConfigException : Syntax error in JSON file /tmp/loader_....json.
Any tips fo this? Also, this command produced a ton of loader.json files that took up a lot of space, so I'm wondering how to avoid this.
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