DeepTrio Best Practices for Quartet Families

[mr-eyes]

I’m working with family quartets (mother, father, proband, and one unaffected sibling) and planning to use DeepTrio for variant calling. Since DeepTrio generates VCFs for each trio configuration, that means the parents will be processed twice — once with the proband trio, and again with the sibling trio.

Is there a best practice for handling this situation to avoid redundant computation?

Thank you!

[lucasbrambrink]

Hi,

Thanks for the question. In this case, you could consider setting --skip_parent_calling for the sibling trio. This would avoid calling the parent samples again. I should note that the call sets wouldn't be identical since the child sample is part of the pileup during parent calling. However, the difference is likely to be small.

Hope that helps!

[mr-eyes]

@lucasbrambrink Oh, I see. I am testing the two approaches and will compare the differences. If significant, I will call them twice, then merge them to get a more inclusive variants list. Otherwise, will use the skip_parent_calling flag. Many thanks!