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Call variant from RNA-Seq data using Haplotypecaller

My understanding is that Haplotypecaller is specifically designed to call variant from DNA-Seq data. However, RNA-Seq has different (more complicated) allele frequency. How comes that Haplotypecaller is still being used in RNA-Seq variant calling pipeline? Can anyone share some information on this question? Really appreciated

Issue · Github
by Sheila

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @UniCorn, if you mean you're concerned that variations in allele expression might unduly influence the calls, you're right -- that's one of the challenges of variant discovery in RNAseq. We currently don't have a good way to account for that in our calling model, so it's a limitation to keep in mind when analyzing results produced by HaplotypeCaller. That being said there is some development work underway to improve our RNAseq toolchain; updates will be posted on our blog when the improvements become available.

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