Compare results of test pipelines with the ones from GIAB

Question

[noff.polina]

Hi all!

I am working on pipeline optimization for WES analysis. I am testing my pipelines on the GIAB sample from the woman from Utah. In order to estimate the quality of my pipelines, I want to compare vcf results to the validated ones. I thought to proceed this through building confusion matrices and calculation of precision and recall parameters and further comparing them to the gold standard.

So my question is, first, is it a good way to compare pipelines? If yes, is there a special command to calculate the parameters of interest or it's usually dome manually?

Maybe I missed some details so don't hesitate to correct me. Thanks!

Answer 1

[finswimmer]

I have made good experiences with hap.py. It is also available in the bioconda repository, which I would strongly recommend for installing.