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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.

How to get the idetail of regions getting fixed during Split'N'Trim step

I am following GATK procedure given at . After doing all step wise analysis, I am curious to check regions getting fixed at Split'N'Trim step. I want to keep the track of those regions so that I can visulise them in IGV.

Also, I have skipped step 4 and step 5 i.e 4. Indel Realignment (optional) and 5. Base Recalibration becuase I am working on RNASEQ data.

But for future reference, I have to deal DNA seq also. How Can I explore the region getting fixed at step 4 and 5 as well.

I just need to have these information in order to understand the impact on my overall analysis.


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