Variant calling with RNA-seq

Hello, I was wondering whether there is a generally used pipeline for variant calling on RNA-seq data within galaxy. I have seen the GATK pipeline using Split’N’Cigar reads and Haplotype caller but I do not currently see these tools on Galaxy. After using STAR for the alignment step, Can I do something as simple as calling Freebayes on the output BAM from STAR, or do I need a specific splice aware variant caller? thanks

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Excellent question!
There is https://github.com/ekg/freebayes/issues/427 suggesting that Freebayes should be able to handle this task, but I haven’t tried this myself yet. I would be very much interested in this since I was planning to experiment with exactly this approach and maybe to write a training tutorial on the topic.

Specifically, the issue above refers to this comment from Erik Garrison, FreeBayes developer.

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