FLARE: Recovering Haplotypes Disrupted by Statistical Phasing

[la-mendicino]

Hi Atkinson Lab,

Do you have plans to make the python scripts for recovering haplotypes disrupted by statistical phasing for FLARE output? That would be a great help, thanks!

Lucas

[shahnirav1005]

Have you checked out extract_tracts_flare.py? https://github.com/Atkinson-Lab/Tractor/tree/master/scripts

[la-mendicino]

I'm referring to Step 0 [Optional]: Recovering Haplotypes Disrupted by Statistical Phasing which is setup only for RFMIX.

[nirav572]

Hi Lucas,

Thanks for the clarification. We don't have plans to extend the haplotype recovery scripts for FLARE beyond the current RFMIX setup at this time, but it’s something we could potentially consider in the future. Additionally, the recovery step is currently optimized only for 2-way analysis, so we've been skipping it for our 3-way analyses. Since you're using FLARE, you could consider skipping this step as well.

Hope that helps!
Nirav