Question: Need recommendations of RNA-Seq somatic variant calling pipeline
gravatar for Zhenyu Zhang
4 months ago by
Zhenyu Zhang260
United States
Zhenyu Zhang260 wrote:

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 variant somatic • 218 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by Zhenyu Zhang260

Umm... this was updated July 2019

ADD REPLYlink modified 4 months ago • written 4 months ago by swbarnes27.5k

hmmm, they still have THIS online, though, which I mention here: A: Inferring genotype based on RNA sequnces

ADD REPLYlink written 4 months ago by Kevin Blighe54k

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.

ADD REPLYlink written 4 months ago by ATpoint29k
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