Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.mergedReg2Map 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.mergedReg2Map.AFR.7 \ --bfile /tmp/ldsc-2024-06-24-2W1a47mH8L/1000G.AFR.HM3.7 \ --thin-annot \ --annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.7.annot.gz \ --l2 \ --ld-wind-kb 1000.0 Beginning analysis at Mon Jun 24 14:11:57 2024 Read list of 66261 SNPs from /tmp/ldsc-2024-06-24-2W1a47mH8L/1000G.AFR.HM3.7.bim Read 1 annotations for 66261 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.7.annot.gz Read list of 661 individuals from /tmp/ldsc-2024-06-24-2W1a47mH8L/1000G.AFR.HM3.7.fam Reading genotypes from /tmp/ldsc-2024-06-24-2W1a47mH8L/1000G.AFR.HM3.7.bed After filtering, 66261 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 66261 SNPs will be printed. Writing LD Scores for 66261 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.7.l2.ldscore.gz Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.7.l2.ldscore.gz MAF L2 mean 0.2278 1.7533 std 0.1459 1.8794 min 0.0015 -0.0837 25% 0.1014 0.5165 50% 0.2171 1.1859 75% 0.3502 2.3010 max 0.5000 17.0179 MAF/LD Score Correlation Matrix MAF L2 MAF 1.0000 0.1205 L2 0.1205 1.0000 Annotation Correlation Matrix ANNOT ANNOT 1.0 Annotation Matrix Column Sums ANNOT 10691 Summary of Annotation Matrix Row Sums count 66261.0000 mean 0.1613 std 0.3679 min 0.0000 25% 0.0000 50% 0.0000 75% 0.0000 max 1.0000 Analysis finished at Mon Jun 24 14:14:26 2024 Total time elapsed: 2.0m:28.18s Done.