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How to evaluate variants

mahyarheymahyarhey BostonMember

I have 33 samples (VCF files) resulted from HaplotypeCaller and like to evaluate them using dbSNP as a comp to get concordance_rate, sensitivity, and specificity. One way is to evaluate each sample separately. Another approach is to combine all 33 files using "CombineGVCFs" and then evaluate one VCF file. Which of these 2 methods do you think is feasible and acceptable for variant evaluation? why? Thanks


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I'm afraid neither approach is really any good (or in 3/4 cases, even valid), for different reasons depending on whether your HC output files are VCFs or GVCFs, and depending on what you are trying to do.

    We've already answered many of your questions and pointed you to the best practices docs multiple times, @mahyarhey . By now you should at least know to express yourself more precisely, use the correct terms and provide more context information when you post your question. We can't continue to spend time helping you if you don't help yourself a little bit first.

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