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Need recommendations of RNA-Seq somatic variant calling pipeline

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.

rna-seq somatic variant
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written by Zhenyu Zhang Zhenyu Zhang

You can probably use their pipeline but treat the results with case, and if you make strong claims on some variants, be sure to verify with either targeted resequencing or Sanger in an appropriate specimen.

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written by ATpoint ATpoint

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