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 EUR. ********************************************************************* * 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.EUR.16 \ --bfile /tmp/ldsc-2024-06-24-USljsiLVEA/1000G.EUR.HM3.16 \ --thin-annot \ --annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.16.annot.gz \ --l2 \ --ld-wind-kb 1000.0 Beginning analysis at Mon Jun 24 13:09:09 2024 Read list of 36853 SNPs from /tmp/ldsc-2024-06-24-USljsiLVEA/1000G.EUR.HM3.16.bim Read 1 annotations for 36853 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.16.annot.gz Read list of 503 individuals from /tmp/ldsc-2024-06-24-USljsiLVEA/1000G.EUR.HM3.16.fam Reading genotypes from /tmp/ldsc-2024-06-24-USljsiLVEA/1000G.EUR.HM3.16.bed After filtering, 36853 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 36853 SNPs will be printed. Writing LD Scores for 36853 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.16.l2.ldscore.gz Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.16.l2.ldscore.gz MAF L2 mean 0.2371 0.4266 std 0.1434 0.9847 min 0.0020 -0.0619 25% 0.1113 0.0014 50% 0.2286 0.0423 75% 0.3588 0.3305 max 0.5000 8.6349 MAF/LD Score Correlation Matrix MAF L2 MAF 1.0000 0.0232 L2 0.0232 1.0000 Annotation Correlation Matrix ANNOT ANNOT 1.0 Annotation Matrix Column Sums ANNOT 729 Summary of Annotation Matrix Row Sums count 36853.0000 mean 0.0198 std 0.1392 min 0.0000 25% 0.0000 50% 0.0000 75% 0.0000 max 1.0000 Analysis finished at Mon Jun 24 13:11:26 2024 Total time elapsed: 2.0m:17.04s Done.