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AI-sandbox / XGMix

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Output - Local Ancestry of each individual marker #14

Closed guidebortoli closed 3 years ago

guidebortoli commented 3 years ago

Hi, I have ran the XGMix in a set of admixed samples that I have simulated for whom I know the true ancestry for each of the individual markers and the switch points.

I noticed that the output of XGMix is given in intervals of genetic positions and I'm wondering if there's a way for the program to give the local ancestry for each individual marker? If a sum all the markers from all the ranges generated I get all the markers from the intersecting SNPs. But this information is not much useful for downstream analysis as I believe the individual maker's ancestry is important...

The same happens with the probability output file: Is there a way to have the probability of individual markers to belong to a certain ancestry?

I'm asking because I intent to use Local Ancestry Inference in conjunction with the Tractor program that allow to include LAI tracks for association analysis and etc...

Thank you!

weekend37 commented 3 years ago

Hi guidebortoli! Transforming the output into the individual markers you have shouldn't be too hard with standard python but this is a good feature request. We've just launched a new codebase, Gnomix, where I'll make sure to add this feature this very week.