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CombineVariants for different samples

lalirlalir CanadaMember

Hello everyone,
I have used the ion proton system to sequence 15 sample exomes so far. In this system, only 3 samples can be run at a given time, so I essentially have five sets of samples. Is it still possible to use CombineVariants on the VCF files of samples that were from different sequencing runs?
Thank you,


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Ricky,

    In general, yes it is possible. Whether it is appropriate to do so, is a different matter. It depends at what stage of processing you want to combine them, and what information you intend to get from them. For example, you cannot run VQSR (variant recalibration) on variants that were not called or joint-genotyped together. But if you have variants that are already filtered and you just want them in the same file for further downstream analysis, then it is ok.

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