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Varinat calling from Multisample RNAseq data???

Hi there,

we are working on 454 RNaseq data......we have RNAseq data of four different tissues from six different individuals.... we want to call variants from all these data in a one job....but as per your recommendation we have to run each tissue data from each individual my query is can we join them as per the DNAseq guidelines or we have to find out some another way to do this kind of analysis....
Please help us if you have any suggestions to do Multisample Variant calling from RNAseq data.....

Best Regards


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @tejas,

    Some of our users have been using the HaplotypeCaller GVCF-based workflow with the RNAseq-specific adaptations. That is ultimately what we are working towards, but at the moment we have not yet validated this method, so we can't guarantee this will work properly. If you try it, please evaluate your results carefully.

  • tejastejas Member

    Thank you for your quick reply...


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