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Is GATK CalculateGenotypePosteriors useful for de novo family mutations?

I have a few WGS samples; patient, mother, father and brother. I am interested in looking for de novo mutations in the patient within the family. My data is a recalibrated variants from GATK VQSR.

The Genotype Refinement workflow from GATK looks promising for finding the mutations (https://software.broadinstitute.org/gatk/documentation/article.php?id=4723).

... (e.g. in the case of loss of function) or with the transmission (or de novo origin) of a variant in a family.

The first step in the workflow is the CalculateGenotypePosteriors tool. In the documentation:

Using the default behavior, priors will only be applied for each variants (provided each variant has at least 10 called samples.)...

Q1: This is where I am not sure. I only have 4 WGS samples in a family, it's not a large scale population analysis. 4 < 10, does that mean the tool is not designing to work for my samples? The Bayesian not designed for just 4 samples in a family?

Q2: If the tool is not appropriate for a family analysis. What would be a better workflow?

Answers

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