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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


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