Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Using Tophat "accepted_hits.bam" file for RNAseq variant calling with GATK

Hi, I have some doubts about variant calling in RNAseq data.

So far, I have aligned the reads to a reference (human hg38) genome using Tophat. However, I have seen in your workflow for variant discovery in RNAseq that you recommend to use STAR. Is this really necessary? Could I use the "accepted_hits.bam" file from Tophat instead of the STAR output? would the rest of the workflow remain the same?

Thanks for your help

Best Answer

Answers

Sign In or Register to comment.