Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.Oligo.hg38 bed regions making annot file Computing partitioned LD scores for hg38 for AFR. ********************************************************************* * LD Score Regression (LDSC) * Version 1.0.1 * (C) 2014-2019 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 /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_EUR_Phase3_GRCh38_files/hapmap3_snps/listHM3.noMHC.txt \ --out /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.AFR.2 \ --bfile /tmp/ldsc-2024-06-24-qWnnPokbtb/1000G.AFR.HM3.2 \ --thin-annot \ --annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.AFR.2.annot.gz \ --l2 \ --ld-wind-kb 1000.0 Beginning analysis at Mon Jun 24 13:08:30 2024 Read list of 100252 SNPs from /tmp/ldsc-2024-06-24-qWnnPokbtb/1000G.AFR.HM3.2.bim Read 1 annotations for 100252 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.AFR.2.annot.gz Read list of 661 individuals from /tmp/ldsc-2024-06-24-qWnnPokbtb/1000G.AFR.HM3.2.fam Reading genotypes from /tmp/ldsc-2024-06-24-qWnnPokbtb/1000G.AFR.HM3.2.bed After filtering, 100252 SNPs remain Estimating LD Score. Reading list of 1215001 SNPs for which to print LD Scores from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_EUR_Phase3_GRCh38_files/hapmap3_snps/listHM3.noMHC.txt After merging with --print-snps, LD Scores for 100252 SNPs will be printed. Writing LD Scores for 100252 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.AFR.2.l2.ldscore.gz Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.AFR.2.l2.ldscore.gz MAF L2 mean 0.2298 0.2437 std 0.1451 0.4882 min 0.0015 -0.0520 25% 0.1044 0.0158 50% 0.2209 0.0617 75% 0.3525 0.2217 max 0.5000 6.2105 MAF/LD Score Correlation Matrix MAF L2 MAF 1.0000 0.0646 L2 0.0646 1.0000 Annotation Correlation Matrix ANNOT ANNOT 1.0 Annotation Matrix Column Sums ANNOT 2105 Summary of Annotation Matrix Row Sums count 100252.0000 mean 0.0210 std 0.1434 min 0.0000 25% 0.0000 50% 0.0000 75% 0.0000 max 1.0000 Analysis finished at Mon Jun 24 13:13:45 2024 Total time elapsed: 5.0m:14.3s Done.