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?