LDSC for each of the 1703 regions defined by ldetech (Joseph K Pickrell 2016)

[jielab]

Hi, I am trying to run LDSC for each of the 1703 regions defined by ldetech (Joseph K Pickrell 2016).

It seems that I first need to run make_annot.py --bed-file ldetech.EUR.bed --bimfile MY.bim --annot-file MY.output.

However, when I run that command, I got an error of sys:1: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False. and my output file only has a column with a header of ANNOT.

Can you please let me know how to run this step correctly? If this is simply assign MY.bim into different regions based on ldetech.EUR.bed, I feel that I could do this by using bedtools, correct?

How to run ldsc.py once the above step is successfully run, so that it calcualtes h2 for each of the 1703 regions?

Thank you & best regards,
Jie