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odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool
https://odelaneau.github.io/shapeit5/
MIT License
61 stars 9 forks source link

Genetic map file for T2T genome (CHM13) #54

Closed hangsuUNC closed 1 year ago

hangsuUNC commented 1 year ago

Hi,

Thanks for this wonderful tool! I was trying to use Shapeit5 for phasing a set of samples processed based on the new released T2T human genome (CHM13). Could you please help pointing the right genetic mapping files? I can only find b37 and b38 genomes in the folder.

Thanks very much for your help!

Hang

srubinacci commented 1 year ago

Hi,

We do not have T2T maps available in this repo yet, but you can liftover the provided maps to the T2T reference. I have also seen a publicly available github repo (https://github.com/JosephLalli/phasing_T2T/tree/master) maintained by Joseph Lalli providing lifted over maps. Just, before using them, please make sure with Joseph you are allowed to.

Simone

hangsuUNC commented 1 year ago

Thanks for the information! This is very helpful! will do!

Hi,

We do not have T2T maps available in this repo yet, but you can liftover the provided maps to the T2T reference. I have also seen a publicly available github repo (https://github.com/JosephLalli/phasing_T2T/tree/master) maintained by Joseph Lalli providing lifted over maps. Just, before using them, please make sure with Joseph you are allowed to.

Simone