ULTIMATE solution (March 20th 2019):
-Make sure rsIDs match between bim file and GWAS SS file
-The chromosome column for both the .bim file and the GWAS SS file need to be numeric (don't add "chr" or "chrom_")
The files are in /oak/stanford/groups/euan/projects/risk_scores/step1_anna
MEGASTROKE_AIS.tsv is the GWAS SS (numeric chr column) and correct rsIDs
step1_UKBB_random2k.sh is the nano file for the script using the random 2000 UKBB participants as the LD reference sample (step1_UKBB_afib.sh is the same using the UKBB participants with Afib i.e. our validation dataset).
step1_ldpred_UKBB_random is the coordinated hdf5 file (output from LDpred step1) (step1_ldpred_UKBB_Afib is the equivalent)
random.e is the file the prints any error text that would be listed from the model (afib.e is the equivalent)
random.o is the file that prints any output text that would be listen from the model (afib.o is the equivalent).
ULTIMATE solution (March 20th 2019): -Make sure rsIDs match between bim file and GWAS SS file -The chromosome column for both the .bim file and the GWAS SS file need to be numeric (don't add "chr" or "chrom_")
The files are in /oak/stanford/groups/euan/projects/risk_scores/step1_anna
MEGASTROKE_AIS.tsv is the GWAS SS (numeric chr column) and correct rsIDs step1_UKBB_random2k.sh is the nano file for the script using the random 2000 UKBB participants as the LD reference sample (step1_UKBB_afib.sh is the same using the UKBB participants with Afib i.e. our validation dataset). step1_ldpred_UKBB_random is the coordinated hdf5 file (output from LDpred step1) (step1_ldpred_UKBB_Afib is the equivalent) random.e is the file the prints any error text that would be listed from the model (afib.e is the equivalent) random.o is the file that prints any output text that would be listen from the model (afib.o is the equivalent).