I am looking for a somatic RNA-Seq variant calling pipeline, that can take tumor RNA-Seq without normals for variant calling. We want production pipelines, that means a stable tool instead of a graduate student project no one used after publication.
Currently I have in mind is the GTAK practice, which is not ideal as it's not specifically designed or supported by Broad.
Any suggestions are welcome. And you will benefit from that, b/c we will process through tens of 0thousands of data and make output available publicly to the research community.