Multivariate ld-score regression of 2 traits (SCZ.sumstats.gz BIP.sumstats.gz) began at: 2025-03-05 09:32:11.93851
Reading in LD scores
Read in summary statistics [1/2] from: SCZ.sumstats.gz
Out of 93561 SNPs, 93295 remain after merging with LD-score files
Removing 0 SNPs with Chi^2 > 117.49826; 93295 remain
Read in summary statistics [2/2] from: BIP.sumstats.gz
Out of 92758 SNPs, 92535 remain after merging with LD-score files
Removing 0 SNPs with Chi^2 > 101.96296; 92535 remain
          
Estimating heritability [1/3] for: SCZ.sumstats.gz
     
Please note that the results initially printed to the screen and log file reflect the NON-liability h2 and cov_g. However, a liability conversion is being used for trait SCZ.sumstats.gz when creating the genetic covariance matrix used as input for Genomic SEM and liability scale results are printed at the end of the log file.
     
Heritability Results for trait: SCZ.sumstats.gz
Mean Chi^2 across remaining SNPs: 2.1967
Lambda GC: 1.8372
Intercept: 1.1072 (0.0523)
Ratio: 0.0896 (0.0437)
Total Observed Scale h2: 0.4042 (0.0513)
h2 Z: 7.88
     
Calculating genetic covariance [2/3] for traits: SCZ.sumstats.gz and BIP.sumstats.gz
92323 SNPs remain after merging SCZ.sumstats.gz and BIP.sumstats.gz summary statistics
Results for genetic covariance between: SCZ.sumstats.gz and BIP.sumstats.gz
Mean Z*Z: 0.7932
Cross trait Intercept: 0.1945 (0.0315)
Total Observed Scale Genetic Covariance (g_cov): 0.2513 (0.0279)
g_cov Z: 8.99
g_cov P-value: 2.3865e-19
          
Estimating heritability [3/3] for: BIP.sumstats.gz
     
Please note that the results initially printed to the screen and log file reflect the NON-liability h2 and cov_g. However, a liability conversion is being used for trait BIP.sumstats.gz when creating the genetic covariance matrix used as input for Genomic SEM and liability scale results are printed at the end of the log file.
     
Heritability Results for trait: BIP.sumstats.gz
Mean Chi^2 across remaining SNPs: 1.6342
Lambda GC: 1.5281
Intercept: 1.0032 (0.0349)
Ratio: 0.005 (0.055)
Total Observed Scale h2: 0.295 (0.0302)
h2 Z: 9.78
     
      
Liability Scale Results
     
Liability scale results for: SCZ
Total Liability Scale h2: 0.2231 (0.0283)
Total Liability Scale Genetic Covariance between SCZ and BIP: 0.1511 (0.0168)
     
     
Liability scale results for: BIP
Total Liability Scale h2: 0.1934 (0.0198)
     
      
Genetic Correlation Results
Genetic Correlation between SCZ and BIP: 0.7276 (0.0809)
     
     
LDSC finished running at 2025-03-05 09:32:18.259378
Running LDSC for all files took 0 minutes and 6 seconds