********************************************************************* * 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 \ --h2 /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/AD_Bellenguez_2022.sumstats.gz \ --ref-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.EUR. \ --out /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/conditional/Human_Striatum_snATAC.conditional.AD-Bellenguez_2022.EUR \ --w-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC. \ --print-coefficients Beginning analysis at Fri Jun 28 13:41:15 2024 Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/AD_Bellenguez_2022.sumstats.gz ... Read summary statistics for 1177947 SNPs. Reading reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.EUR.[1-22] ... (ldscore_fromlist) Read reference panel LD Scores for 1198864 SNPs. Removing partitioned LD Scores with zero variance. Reading regression weight LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC.[1-22] ... (ldscore_fromlist) Read regression weight LD Scores for 1198864 SNPs. After merging with reference panel LD, 1165432 SNPs remain. After merging with regression SNP LD, 1165432 SNPs remain. Removed 0 SNPs with chi^2 > 487.511 (1165432 SNPs remain) Total Observed scale h2: 0.0211 (0.003) Categories: Human_Striatum_snATAC.Astro.hg38_0 Human_Striatum_snATAC.D1.D2H.hg38_1 Human_Striatum_snATAC.D1.Matrix.hg38_2 Human_Striatum_snATAC.D1.Striosome.hg38_3 Human_Striatum_snATAC.D2.Matrix.hg38_4 Human_Striatum_snATAC.D2.Striosome.hg38_5 Human_Striatum_snATAC.INT.hg38_6 Human_Striatum_snATAC.Microglia.hg38_7 Human_Striatum_snATAC.Oligo.hg38_8 Human_Striatum_snATAC.OPC.hg38_9 Human_Striatum_snATAC.mergedReg2Map_10 Coding_UCSCL2_11 Coding_UCSC.extend.500L2_11 Conserved_LindbladTohL2_11 Conserved_LindbladToh.extend.500L2_11 CTCF_HoffmanL2_11 CTCF_Hoffman.extend.500L2_11 DGF_ENCODEL2_11 DGF_ENCODE.extend.500L2_11 DHS_peaks_TrynkaL2_11 DHS_TrynkaL2_11 DHS_Trynka.extend.500L2_11 Enhancer_AnderssonL2_11 Enhancer_Andersson.extend.500L2_11 Enhancer_HoffmanL2_11 Enhancer_Hoffman.extend.500L2_11 FetalDHS_TrynkaL2_11 FetalDHS_Trynka.extend.500L2_11 H3K27ac_HniszL2_11 H3K27ac_Hnisz.extend.500L2_11 H3K27ac_PGC2L2_11 H3K27ac_PGC2.extend.500L2_11 H3K4me1_peaks_TrynkaL2_11 H3K4me1_TrynkaL2_11 H3K4me1_Trynka.extend.500L2_11 H3K4me3_peaks_TrynkaL2_11 H3K4me3_TrynkaL2_11 H3K4me3_Trynka.extend.500L2_11 H3K9ac_peaks_TrynkaL2_11 H3K9ac_TrynkaL2_11 H3K9ac_Trynka.extend.500L2_11 Intron_UCSCL2_11 Intron_UCSC.extend.500L2_11 PromoterFlanking_HoffmanL2_11 PromoterFlanking_Hoffman.extend.500L2_11 Promoter_UCSCL2_11 Promoter_UCSC.extend.500L2_11 Repressed_HoffmanL2_11 Repressed_Hoffman.extend.500L2_11 SuperEnhancer_HniszL2_11 SuperEnhancer_Hnisz.extend.500L2_11 TFBS_ENCODEL2_11 TFBS_ENCODE.extend.500L2_11 Transcr_HoffmanL2_11 Transcr_Hoffman.extend.500L2_11 TSS_HoffmanL2_11 TSS_Hoffman.extend.500L2_11 UTR_3_UCSCL2_11 UTR_3_UCSC.extend.500L2_11 UTR_5_UCSCL2_11 UTR_5_UCSC.extend.500L2_11 WeakEnhancer_HoffmanL2_11 WeakEnhancer_Hoffman.extend.500L2_11 Observed scale h2: -0.0017 -0.0005 -0.0011 0.0028 0.0015 -0.003 -0.0002 0.0069 0.0018 -0.0015 -0.0009 0.0005 0.0052 0.0015 -0.0077 0.0039 -0.0023 0.0035 -0.0074 -0.002 -0.0031 0.0096 0.0009 -0.0012 -0.0002 -0.0004 0.0013 -0.0079 0.0095 -0.0038 0.0094 -0.0059 0.0063 -0.0136 0.0101 -0.0015 0.0118 -0.0068 0.0023 -0.0018 -0.0038 -0.0235 0.0235 0.001 -0.0021 -0.0046 0.0044 0.0016 -0.0077 -0.0073 0.0071 0.0003 0.0059 -0.0021 0.0091 -0.0016 0.0041 0.0006 -0.0011 -0.0016 0.0013 -0.0003 0.0035 Observed scale h2 SE: 0.0009 0.001 0.002 0.0019 0.0019 0.002 0.0012 0.0022 0.0018 0.0011 0.0034 0.0019 0.0025 0.0014 0.0041 0.0013 0.0018 0.0032 0.0085 0.0047 0.0059 0.0101 0.0007 0.0009 0.0021 0.0034 0.0032 0.0059 0.0136 0.0139 0.0101 0.0093 0.0046 0.0091 0.0097 0.0014 0.0042 0.0055 0.0016 0.0048 0.0053 0.0277 0.0293 0.0006 0.0013 0.0046 0.0048 0.0057 0.0076 0.0353 0.036 0.0042 0.0048 0.0049 0.008 0.002 0.0027 0.0012 0.0014 0.0009 0.0016 0.0014 0.0023 Proportion of SNPs: 0.0024 0.0016 0.0043 0.0032 0.0041 0.0031 0.0029 0.0019 0.0019 0.0024 0.0123 0.0026 0.0084 0.0041 0.0362 0.0022 0.0062 0.0149 0.0501 0.0135 0.02 0.0486 0.0004 0.0018 0.0044 0.0085 0.0104 0.0292 0.0364 0.0388 0.026 0.0314 0.0185 0.0434 0.0567 0.0042 0.0132 0.0232 0.0041 0.0131 0.022 0.0345 0.036 0.0008 0.003 0.0046 0.0055 0.0346 0.0553 0.0158 0.016 0.0136 0.0321 0.029 0.0616 0.0017 0.0031 0.0018 0.0035 0.0007 0.0031 0.0023 0.0085 Proportion of h2g: -0.0789 -0.0221 -0.052 0.131 0.0733 -0.1431 -0.0089 0.3275 0.0863 -0.0722 -0.0407 0.0217 0.2479 0.0732 -0.3622 0.1835 -0.1083 0.1642 -0.3503 -0.0965 -0.1465 0.4541 0.0435 -0.0568 -0.0092 -0.0167 0.0611 -0.3755 0.4515 -0.1815 0.4452 -0.2773 0.2983 -0.642 0.4772 -0.0701 0.5574 -0.3224 0.1088 -0.083 -0.1807 -1.1116 1.1114 0.0454 -0.0984 -0.2196 0.2069 0.0756 -0.3657 -0.345 0.334 0.0154 0.2811 -0.0972 0.429 -0.0765 0.1935 0.028 -0.0537 -0.0746 0.0613 -0.0136 0.1655 Enrichment: -32.2885 -13.5962 -12.2227 40.4649 17.8922 -46.494 -3.0887 170.5894 45.9437 -30.1539 -3.2968 8.213 29.4439 17.8977 -9.994 83.3161 -17.3867 10.9903 -6.9918 -7.1566 -7.3358 9.3522 97.8194 -31.2625 -2.1112 -1.9708 5.8628 -12.8481 12.4091 -4.6763 17.1128 -8.819 16.1045 -14.7932 8.4219 -16.522 42.1736 -13.9176 26.4845 -6.3353 -8.1935 -32.212 30.8603 55.5826 -33.1808 -47.895 37.6351 2.1855 -6.6098 -21.8571 20.8481 1.1337 8.7612 -3.3506 6.962 -45.6779 62.6562 15.8328 -15.4198 -101.3019 20.0481 -5.8788 19.3779 Coefficients: -5.1562e-08 -2.1712e-08 -1.9519e-08 6.4619e-08 2.8572e-08 -7.4247e-08 -4.9324e-09 2.7242e-07 7.3369e-08 -4.8153e-08 -5.2647e-09 1.3115e-08 4.7020e-08 2.8581e-08 -1.5960e-08 1.3305e-07 -2.7765e-08 1.7551e-08 -1.1165e-08 -1.1429e-08 -1.1715e-08 1.4935e-08 1.5621e-07 -4.9924e-08 -3.3713e-09 -3.1472e-09 9.3624e-09 -2.0517e-08 1.9816e-08 -7.4677e-09 2.7328e-08 -1.4083e-08 2.5718e-08 -2.3624e-08 1.3449e-08 -2.6384e-08 6.7348e-08 -2.2225e-08 4.2294e-08 -1.0117e-08 -1.3084e-08 -5.1440e-08 4.9282e-08 8.8761e-08 -5.2987e-08 -7.6485e-08 6.0100e-08 3.4901e-09 -1.0555e-08 -3.4904e-08 3.3293e-08 1.8104e-09 1.3991e-08 -5.3506e-09 1.1118e-08 -7.2944e-08 1.0006e-07 2.5284e-08 -2.4624e-08 -1.6177e-07 3.2015e-08 -9.3880e-09 3.0945e-08 Coefficient SE: 2.8682e-08 4.6240e-08 3.4879e-08 4.3270e-08 3.5675e-08 5.0153e-08 3.1274e-08 8.7515e-08 7.0394e-08 3.4853e-08 2.0793e-08 5.4980e-08 2.2591e-08 2.5021e-08 8.6062e-09 4.6202e-08 2.1626e-08 1.6014e-08 1.2757e-08 2.6140e-08 2.2231e-08 1.5739e-08 1.1741e-07 3.8281e-08 3.5626e-08 3.0331e-08 2.3140e-08 1.5217e-08 2.8216e-08 2.7126e-08 2.9287e-08 2.2226e-08 1.8768e-08 1.5797e-08 1.2948e-08 2.5288e-08 2.4143e-08 1.8008e-08 3.0125e-08 2.7693e-08 1.8246e-08 6.0619e-08 6.1391e-08 5.9039e-08 3.2155e-08 7.6227e-08 6.5301e-08 1.2417e-08 1.0346e-08 1.6895e-07 1.6954e-07 2.3338e-08 1.1372e-08 1.2877e-08 9.8515e-09 8.9347e-08 6.6595e-08 5.2256e-08 3.0238e-08 9.5780e-08 3.8765e-08 4.6725e-08 2.0020e-08 Lambda GC: 1.2005 Mean Chi^2: 1.272 Intercept: 1.0742 (0.0253) Ratio: 0.2728 (0.0929) Analysis finished at Fri Jun 28 13:44:08 2024 Total time elapsed: 2.0m:53.12s