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

I am following GATK procedure given at https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq . 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.

Answers

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