Inquiry about the GATK Best Practices for variant calling on RNAseq

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Benjamin Hing

• July 02, 2020 00:24

Hi,

I was wondering if I could get your help to track down a previous webpage that details a step by step workflow for the GATK Best Practices for variant calling on RNA-seq data. Part of the original post can be found here: https://gatkforums.broadinstitute.org/gatk/discussion/3892/the-gatk-best-practices-for-variant-calling-on-rnaseq-in-full-detail 

There used to be a hyperlink that takes the reader to another page that had a very detailed explanation of all the code used to run the workflow in a very systematic way. I was working through it in 2018 but I don't seem to be able to find the webpage again. I was wondering if I could get some help with tracking down that website that contains the detailed explanation?

 

Thanks!

 

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  Genevieve Brandt (she/her)

  • July 02, 2020 20:00

  Hi Benjamin Hing, I am not sure specifically what hyperlink you are referring to, but we have a new documentation website. The best practices for RNA seq short variant discovery is here . We also have the legacy forum available here, you can check and see if the page you are thinking of is there.

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