Finding Recombination Breakpoints using Hail

Hello all! I am trying to find a way to find recombination breakpoints in a family trio with Hail. I am trying to find a row of markers that are present in one parent only, and then transition to a row of markers that are present in another parent. Can I ask if there are any possible Hail functions that might be useful? Thank you so much.

This is something Hail doesn’t support right now, unfortunately. Hail currently parallelizes data by genomic interval, and algorithms like this that require backward/forward information are tricky to write.

Thank you so much for your response! For the “backward/forward information”, does it mean that it is not feasible to write, or is it too computationally expensive?

It’s certainly feasible (anything is feasible!) but it’s not a priority. I don’t expect Hail to support this in the next year, for instance.

It’s certainly possible to export chunks of data as VCFs and run other tools to compute these metrics, then load those metrics back into Hail.

Great! I know that this might be a lot to ask, but do you know any possible methods to find an inheritance block (of variants) in an individual, that is only present in one of the parents? I am scanning through the methods but I am not able to find a viable function.

I don’t think this exists in Hail, no. Sorry!