Need recommendations of RNA-Seq somatic variant calling pipeline

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4.6 years ago

Zhenyu Zhang ★ 1.2k

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 • 1.2k views

ADD COMMENT • link 4.6 years ago by Zhenyu Zhang ★ 1.2k

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Umm... this was updated July 2019

https://software.broadinstitute.org/gatk/best-practices/

ADD REPLY • link 4.6 years ago by swbarnes2 14k

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

ADD REPLY • link 4.6 years ago by Kevin Blighe 87k

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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 REPLY • link 4.6 years ago by ATpoint 82k

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