GQ in jointly genotyped samples

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stelmaria

• July 29, 2021 21:11

I followed the "Germline short variant discovery" Best Practices to first call variants per-sample and then jointly genotype them. Does the reported genotype confidence (GQ) of a sample depend on the genotypes observed in the other samples used in the joint genotyping (e.g., would the confidence in a genotype be higher if the variant was observed in multiple samples rather than in a single sample)? 

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  Genevieve Brandt (she/her)

  • August 03, 2021 23:03

  Hi stelmaria,

  Yes, the GQ can change because it depends on the PLs. These are recomputed when running GenotypeGVCFs. There are a variety of resources that describe this, here are some links to look at:

  • https://gatk.broadinstitute.org/hc/en-us/articles/360035890451-Calculation-of-PL-and-GQ-by-HaplotypeCaller-and-GenotypeGVCFs
  • https://gatk.broadinstitute.org/hc/en-us/articles/360035531532

  Generally most calls will be similar than if you ran individual sample calling but variants that are on the borderline can see differences.

  Let me know if you have further questions.

  Best,

  Genevieve

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