Which baseline model was used to generate the sclinker's annotation files

[baosuying]

Hi @kkdey,

Thanks for sharing the sc-linker and LD score resource files, they are super useful. I recently tried to use the sclinker's annotation files under Jagadeesh_Dey_sclinker/annotations/cell_type_programs and used the baselineLD_v2.1_annots as suggested, but always got the following error:

"ValueError: Missing some LD scores from cts files. Are you sure all SNPs in ref-ld-chr are also in ref-ld-chr-cts"

I checked the l2.ldscore files for both, and noticed the SNPs in annotation's l2.ldscore files are not consistent with that in baseline model. For example, for chr6, there are 75358 SNPs in baselineLD.6.l2.ldscore.gz, but there are 80219 SNPs in all annotations' *.6.l2.ldscore.gz files

Which baseline version should I use to smoothly apply these annotation files? Pls advice.

Thanks!