RNA Mutect Pipeline
Answered
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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Hi D,
I am going to move your post into our Community Discussions -> General Discussion topic, as the somatic topic is for reporting bugs and issues with GATK.
You can read more about our forum guidelines and the topics here: Forum Guidelines.
Best,
Pamela
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Hi D,
Thanks for writing into the GATK forum! Our group does not support the pipeline you are referring to, it looks like it is made at the broad institute but it is not one of our featured workspaces. We don't currently have a RNA somatic best practices pipeline available. I would recommend seeing if other researchers have experience with this use case and can advise, and also reaching out to the developer of that pipeline on github. There may be some related discussions on this forum so you may want to do some digging to find more info.
Sorry we don't have more information!
Best,
Genevieve
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