At which stage family genotype posterior recommened in germline discovery best practice?

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Adi Abuali

• April 01, 2021 10:56

I have 4 samples (Father, Mother, son, grandson), and am trying to refine the calling using family.ped using CalculateGenotypePosteriors, and also referring to https://gatk.broadinstitute.org/hc/en-us/articles/360035890411-Calling-variants-on-cohorts-of-samples-using-the-HaplotypeCaller-in-GVCF-mode . I would like to clarify the following: 1-Should this be done before joint calling using GenotypeGVCFs or after and before VQSR? 2-When define family.ped , this confirmed to be restricted to mother, father, and son, and no grandson definition can be added? 3-If the aim to refine all the 4 samples, so which need to be defined as affected?

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  Genevieve Brandt (she/her)

  • April 16, 2021 19:15

  Hi Adi Abuali,

  Have you seen this walk-through of the Genotype Refinement Workflow? I believe it contains the information you are looking for. Please let us know if you have further questions and we can try to expand our existing documentation.

  Best,

  Genevieve

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