********************************************************************* * LD Score Regression (LDSC) * Version 1.0.0 * (C) 2014-2015 Brendan Bulik-Sullivan and Hilary Finucane * Broad Institute of MIT and Harvard / MIT Department of Mathematics * GNU General Public License v3 ********************************************************************* Call: ./ldsc.py \ --print-snps /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.4.snp \ --ld-wind-cm 1.0 \ --out all_da_open_results/train_models/clusters_13-cluster_1.4 \ --bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4 \ --annot all_da_open_results/train_models/clusters_13-cluster_1.4.annot.gz \ --l2 Beginning analysis at Tue Oct 31 17:27:52 2017 Read list of 729645 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4.bim Read 1 annotations for 729645 SNPs from all_da_open_results/train_models/clusters_13-cluster_1.4.annot.gz Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4.fam Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.4.bed Estimating LD Score. Reading list of 85881 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.4.snp After merging with --print-snps, LD Scores for 74259 SNPs will be printed. Writing LD Scores for 74259 SNPs to all_da_open_results/train_models/clusters_13-cluster_1.4.l2.ldscore.gz Summary of LD Scores in all_da_open_results/train_models/clusters_13-cluster_1.4.l2.ldscore.gz MAF L2 mean 0.2367 0.3368 std 0.1431 1.0114 min 0.0051 -0.0909 25% 0.1115 0.0000 50% 0.2301 0.0079 75% 0.3579 0.1302 max 0.5000 18.7276 MAF/LD Score Correlation Matrix MAF L2 MAF 1.0000 0.0363 L2 0.0363 1.0000 Annotation Correlation Matrix SPECIFIC_PEAK_INTERSECT SPECIFIC_PEAK_INTERSECT 1.0 Annotation Matrix Column Sums SPECIFIC_PEAK_INTERSECT 1683 Summary of Annotation Matrix Row Sums count 729645.0000 mean 0.0023 std 0.0480 min 0.0000 25% 0.0000 50% 0.0000 75% 0.0000 max 1.0000 Analysis finished at Tue Oct 31 19:39:53 2017 Total time elapsed: 2.0h:12.0m:0.61s