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Benefits of running UnifiedGenotyper on multiple samples at the same time

The best practice guide states to call variants across all samples simultaneously. Besides the ease of working with one multi-sample VCF, what advantages are there to calling the variants at the same time? Does GATK leverage information across all samples when making calls? If so, what assumptions is the UnifiedGenotyper making about the relationship of these samples to each other, and what are the effects on the variant calls?



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Justin,

    The UG doesn't make any population genetics assumptions about the samples, if that's what you mean. But it does "recognize" when the same variant is present in many samples, which it takes to mean that the variants is more likely to be real than an artefact. So if you have low coverage data, with variants that are not well supported in individual samples, calling many samples together will increase the chance that the UG will call these variants rather than dismiss them as errors.

    Please see this document for the mathematical details of multisample calling:

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