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.9 \ --bfile /tmp/ldsc-2024-06-24-HtI3DgUkhG/1000G.EUR.HM3.9 \ --thin-annot \ --annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.9.annot.gz \ --l2 \ --ld-wind-kb 1000.0 Beginning analysis at Mon Jun 24 13:08:56 2024 Read list of 55879 SNPs from /tmp/ldsc-2024-06-24-HtI3DgUkhG/1000G.EUR.HM3.9.bim Read 1 annotations for 55879 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.9.annot.gz Read list of 503 individuals from /tmp/ldsc-2024-06-24-HtI3DgUkhG/1000G.EUR.HM3.9.fam Reading genotypes from /tmp/ldsc-2024-06-24-HtI3DgUkhG/1000G.EUR.HM3.9.bed After filtering, 55879 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 55879 SNPs will be printed. Writing LD Scores for 55879 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.9.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.9.l2.ldscore.gz MAF L2 mean 0.2342 0.5381 std 0.1431 1.1043 min 0.0020 -0.1030 25% 0.1093 0.0186 50% 0.2227 0.1138 75% 0.3549 0.5517 max 0.5000 11.4181 MAF/LD Score Correlation Matrix MAF L2 MAF 1.0000 0.1103 L2 0.1103 1.0000 Annotation Correlation Matrix ANNOT ANNOT 1.0 Annotation Matrix Column Sums ANNOT 1538 Summary of Annotation Matrix Row Sums count 55879.0000 mean 0.0275 std 0.1636 min 0.0000 25% 0.0000 50% 0.0000 75% 0.0000 max 1.0000 Analysis finished at Mon Jun 24 13:13:13 2024 Total time elapsed: 4.0m:16.25s Done.