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LD_prune_sum_stats.py

LD_prune_sum_stats.py

 
 

README.md

README.md

 
 

analyze_results.py

analyze_results.py

 
 

coordinate_data.py

coordinate_data.py

 
 

h5py_util.py

h5py_util.py

 
 

kgenome.py

kgenome.py

 
 

ld.py

ld.py

 
 

ld_score.py

ld_score.py

 
 

pc_score.py

pc_score.py

 
 

prefilter.py

prefilter.py

 
 

run_analysis.py

run_analysis.py

 
 

slurm.py

slurm.py

 
 

ss_imputation.py

ss_imputation.py

 
 

sum_stats.py

sum_stats.py

 
 

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pypcma

Things to do:

Set up pipeline as follows:

  • Parse summary stats, and obtain per-SNP sample sizes: sum_stats.py
  • Coordinate data for analysis runs: ...
  • Analysis part: ...
  • Results analysis: ...

Other things

  • LD score regression (estimation of covariance matrix):
  • Imputation of summary statistics:

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Multiple-trait analysis

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