********************************************************************* * 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/Glaucoma-Choquet_2018.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.Glaucoma-Choquet_2018.EUR \ --w-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC. \ --print-coefficients Beginning analysis at Mon Jun 24 14:56:48 2024 Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/Glaucoma-Choquet_2018.sumstats.gz ... Read summary statistics for 1195704 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, 1183089 SNPs remain. After merging with regression SNP LD, 1183089 SNPs remain. Removed 54 SNPs with chi^2 > 80 (1183035 SNPs remain) Total Observed scale h2: 5483.2993 (470.8707) 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: 2.9055e+02 2.4631e+02 4.6335e+02 -4.4280e+01 -3.3355e+02 -1.9403e+00 -7.4473e+01 -3.0081e+01 -1.0445e+02 5.1790e+02 -1.5654e+03 -3.1142e+02 -6.7405e+02 1.1975e+03 1.2530e+03 5.6562e+02 -1.4582e+03 7.3965e+02 5.8084e+02 6.5446e+02 1.6699e+03 -5.0355e+01 4.5699e+01 -8.4115e+01 1.2161e+02 -1.4255e+02 -4.3687e+01 -1.7399e+03 -5.7101e+03 6.0647e+03 1.0288e+02 3.9429e+02 -4.0741e+02 1.5939e+03 -7.4227e+02 -2.1535e+02 4.8199e+02 9.7023e+02 1.4915e+02 2.0299e+03 -3.4985e+02 4.7630e+03 -4.5623e+03 2.4984e+02 -4.9617e+02 -2.3644e+02 4.2294e+02 5.2327e+02 -1.9282e+03 1.1340e+03 -5.2330e+02 -6.0057e+01 1.5439e+02 -9.3104e+02 1.5659e+03 -6.4634e+01 -4.1289e+02 5.4644e+02 -5.6479e+02 1.1004e+02 -1.4333e+02 4.5716e+02 -5.7047e+02 Observed scale h2 SE: 263.6171 245.6974 469.121 462.5427 440.3814 420.7729 264.4964 191.3465 247.8934 369.3307 688.4103 294.4895 450.7998 283.0001 816.1919 240.2406 402.3999 840.5256 1684.895 1033.6484 1426.6855 2145.8831 123.1534 214.3868 475.9293 651.5981 879.5902 1167.9147 3034.3123 3240.1903 1487.0336 1623.9505 876.3675 1947.4507 2233.6739 373.9394 824.9582 1132.0072 440.2894 910.6249 1096.6205 2246.1919 2326.5967 157.8849 253.4731 743.6974 770.1961 1559.4206 1714.3323 4394.4459 4359.8921 783.9129 1270.7829 1113.501 1718.6625 292.5537 383.2712 290.6578 349.8329 132.4495 264.7487 287.8392 489.8448 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: 5.2988e-02 4.4920e-02 8.4502e-02 -8.0754e-03 -6.0831e-02 -3.5386e-04 -1.3582e-02 -5.4859e-03 -1.9049e-02 9.4450e-02 -2.8548e-01 -5.6795e-02 -1.2293e-01 2.1840e-01 2.2851e-01 1.0315e-01 -2.6594e-01 1.3489e-01 1.0593e-01 1.1936e-01 3.0455e-01 -9.1834e-03 8.3342e-03 -1.5340e-02 2.2178e-02 -2.5996e-02 -7.9673e-03 -3.1730e-01 -1.0414e+00 1.1060e+00 1.8762e-02 7.1907e-02 -7.4300e-02 2.9068e-01 -1.3537e-01 -3.9273e-02 8.7901e-02 1.7694e-01 2.7200e-02 3.7020e-01 -6.3804e-02 8.6864e-01 -8.3203e-01 4.5564e-02 -9.0487e-02 -4.3120e-02 7.7132e-02 9.5429e-02 -3.5165e-01 2.0681e-01 -9.5435e-02 -1.0953e-02 2.8156e-02 -1.6980e-01 2.8557e-01 -1.1787e-02 -7.5300e-02 9.9654e-02 -1.0300e-01 2.0069e-02 -2.6139e-02 8.3373e-02 -1.0404e-01 Enrichment: 21.6957 27.6237 19.8547 -2.4942 -14.85 -0.115 -4.7072 -2.8577 -10.1362 39.47 -23.127 -21.4802 -14.6028 53.3904 6.3055 46.8375 -42.7101 9.0311 2.1141 8.8528 15.2456 -0.1891 18.759 -8.4386 5.0872 -3.0699 -0.7649 -10.857 -28.623 28.4905 0.7212 2.2869 -4.0118 6.6975 -2.3889 -9.2558 6.6509 7.6389 6.6231 28.2667 -2.8937 25.171 -23.103 55.7413 -30.5154 -9.4062 14.0303 2.7577 -6.355 13.1017 -5.9565 -0.8054 0.8776 -5.8533 4.6339 -7.0398 -24.3767 56.403 -29.5818 27.256 -8.5463 36.0836 -12.1826 Coefficients: 8.9840e-03 1.1439e-02 8.2216e-03 -1.0328e-03 -6.1492e-03 -4.7609e-05 -1.9492e-03 -1.1833e-03 -4.1973e-03 1.6344e-02 -9.5767e-03 -8.8947e-03 -6.0469e-03 2.2108e-02 2.6110e-03 1.9395e-02 -1.7686e-02 3.7397e-03 8.7542e-04 3.6658e-03 6.3131e-03 -7.8318e-05 7.7679e-03 -3.4943e-03 2.1065e-03 -1.2712e-03 -3.1672e-04 -4.4958e-03 -1.1853e-02 1.1798e-02 2.9865e-04 9.4697e-04 -1.6612e-03 2.7733e-03 -9.8921e-04 -3.8327e-03 2.7541e-03 3.1632e-03 2.7425e-03 1.1705e-02 -1.1982e-03 1.0423e-02 -9.5667e-03 2.3082e-02 -1.2636e-02 -3.8950e-03 5.8098e-03 1.1420e-03 -2.6316e-03 5.4253e-03 -2.4665e-03 -3.3351e-04 3.6341e-04 -2.4238e-03 1.9188e-03 -2.9151e-03 -1.0094e-02 2.3356e-02 -1.2250e-02 1.1286e-02 -3.5389e-03 1.4942e-02 -5.0447e-03 Coefficient SE: 0.0082 0.0114 0.0083 0.0108 0.0081 0.0103 0.0069 0.0075 0.01 0.0117 0.0042 0.0084 0.004 0.0052 0.0017 0.0082 0.0049 0.0042 0.0025 0.0058 0.0054 0.0033 0.0209 0.0089 0.0082 0.0058 0.0064 0.003 0.0063 0.0063 0.0043 0.0039 0.0036 0.0034 0.003 0.0067 0.0047 0.0037 0.0081 0.0053 0.0038 0.0049 0.0049 0.0146 0.0065 0.0123 0.0106 0.0034 0.0023 0.021 0.0206 0.0044 0.003 0.0029 0.0021 0.0132 0.0094 0.0124 0.0076 0.0136 0.0065 0.0094 0.0043 Lambda GC: 1.1491 Mean Chi^2: 1.2158 Intercept: 1.0154 (0.0102) Ratio: 0.0713 (0.0472) Analysis finished at Mon Jun 24 14:59:41 2024 Total time elapsed: 2.0m:52.41s