Curate data for genotype, diseases/traits, SNP annotations. See details in job.curate_data#readme.
- Generate simulation parameters:
get_config.ipynb. - Generate simulation data:
s1_simulate_paper.sh. - Run LDSPEC on the simulation data:
s2_regress_paper.sh,s2_regress_paper.vary_winsize.sh. - Make figures:
paper_simulations.main.ipynb,paper_simulations.other_model.ipynb,paper_simulations.vary_winsize.ipynb.
LDSPEC pipeline:
- Compute LD:
gdreg_s1_get_ld.all_1e7.sh,gdreg_s1_get_ld.all_1e7.sh. - Compute sumstats:
ldspec_s2_get_sumstats.sh. - Compute average R for SNP-pair anntoations:
ldspec_s3_get_avgr.sh. - Compute LD scores for single-SNP annotations:
ldspec_s3_get_score_pannot.sh,ldspec_s3_get_score_pannot.vary_winsize.sh. - Run regression:
ldspec_s4_regress.sh.
Compute score correlations: score_corr.ipynb
Figures
- Figures 2,3,5:
paper_main.ipynb - Figure 4:
paper_main.h2enrich_vs_cor.ipynb - Supp. Figures:
paper_main.comparison.ipynb,paper_main.individual_trait.ipynb.