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  • #16
    I do have a set of data containing both Exome Seq and RNA Seq. It will be interesting to see how they correlate in terms of calling. Specifically, it will be interested to see how mark duplication will affect the concordance between the RNA samples from the DNA samples. However, I do have a question: is it valid to use tools like GATK to perform snp calling on RNA Samples? To my knowledge, it seems like GATK might contain certain prior specifically designed for exome sequencing (or whole genome sequencing). Wouldn't that also affect the call concordance in the final data?

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