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  • has anyone tried variant detection with RNA-seq using GATK?

    I'm wondering if anyone has used the GATK tools for variant detection with RNA-seq?

    I have some paired end RNA samples that I want to perform variant detection on and am wondering if I can adapt our GATK exome pipeline for the task which is:
    BWA alignment -> GATK realignment -> Picard duplicates removal -> GATK base quality recalibration-> GATK Unified Genotyper

    The GATK group say in their forum that, while their programs were designed for genomic data, it doesn't mean that they wouldn't work on RNA-seq but they just haven't tried them on that type of data.

    I'd love to know if anyone here has tried them or what your thoughts are on this?

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