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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
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?