Question: Need recommendations of RNA-Seq somatic variant calling pipeline
0
gravatar for Zhenyu Zhang
12 days 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 • 125 views
ADD COMMENTlink modified 12 days ago • written 12 days ago by Zhenyu Zhang260
2

Umm... this was updated July 2019

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

ADD REPLYlink modified 12 days ago • written 12 days ago by swbarnes26.7k

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

ADD REPLYlink written 12 days ago by Kevin Blighe50k

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 12 days ago by ATpoint24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1332 users visited in the last hour