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

Question

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

Opened this issue a year ago · 4 comments

Hi,
I generated cell-type-specific LDScores from bed files using the "1000G_Phase3_EAS_plinkfiles.tgz" from the google cloud and tried to run ldsc.py in the cts mode using the "1000G_EAS_Phase3_baseline_v1.2" but I get the following message:

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've done this analysis using the EUR reference files and everything seems to work just well. Do I need to use different files?

Answer 1 · 2023-07-05T07:56:09.000Z

hi, I had the same error. Did you get it solved? Thanks

Answer 2 · 2023-07-05T15:44:57.000Z

Hi, I couldn't generate matching files, so I manually intersected the ldscore.gz files from the EAS baseline and my custom files. This decreased the number of SNPs in both files so I guess is not ideal, but it allowed me to run the regression.

Answer 3 · 2023-07-06T07:51:10.000Z

Thank you so much for your reply. Could you please kindly provide your code? Thanks again.

Answer 4 · 2023-10-09T08:51:42.000Z

This error may be caused by the mismatch between hapmap3_snps list and EAS baseline. While generating cell type specific LD score with parameter '--print-snps', some snps in baseline model were filtered.