********************************************************************* * 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/OE_vs_UX_EUR-Polimanti_2020.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/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.OE_vs_UX_EUR-Polimanti_2020.EUR \ --w-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC. \ --print-coefficients Beginning analysis at Sat Jun 22 17:10:48 2024 Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/OE_vs_UX_EUR-Polimanti_2020.sumstats.gz ... Read summary statistics for 1000552 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/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, 997142 SNPs remain. After merging with regression SNP LD, 997142 SNPs remain. Removed 0 SNPs with chi^2 > 80 (997142 SNPs remain) Total Observed scale h2: 0.0127 (0.0179) 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 Coding_UCSCL2_10 Coding_UCSC.extend.500L2_10 Conserved_LindbladTohL2_10 Conserved_LindbladToh.extend.500L2_10 CTCF_HoffmanL2_10 CTCF_Hoffman.extend.500L2_10 DGF_ENCODEL2_10 DGF_ENCODE.extend.500L2_10 DHS_peaks_TrynkaL2_10 DHS_TrynkaL2_10 DHS_Trynka.extend.500L2_10 Enhancer_AnderssonL2_10 Enhancer_Andersson.extend.500L2_10 Enhancer_HoffmanL2_10 Enhancer_Hoffman.extend.500L2_10 FetalDHS_TrynkaL2_10 FetalDHS_Trynka.extend.500L2_10 H3K27ac_HniszL2_10 H3K27ac_Hnisz.extend.500L2_10 H3K27ac_PGC2L2_10 H3K27ac_PGC2.extend.500L2_10 H3K4me1_peaks_TrynkaL2_10 H3K4me1_TrynkaL2_10 H3K4me1_Trynka.extend.500L2_10 H3K4me3_peaks_TrynkaL2_10 H3K4me3_TrynkaL2_10 H3K4me3_Trynka.extend.500L2_10 H3K9ac_peaks_TrynkaL2_10 H3K9ac_TrynkaL2_10 H3K9ac_Trynka.extend.500L2_10 Intron_UCSCL2_10 Intron_UCSC.extend.500L2_10 PromoterFlanking_HoffmanL2_10 PromoterFlanking_Hoffman.extend.500L2_10 Promoter_UCSCL2_10 Promoter_UCSC.extend.500L2_10 Repressed_HoffmanL2_10 Repressed_Hoffman.extend.500L2_10 SuperEnhancer_HniszL2_10 SuperEnhancer_Hnisz.extend.500L2_10 TFBS_ENCODEL2_10 TFBS_ENCODE.extend.500L2_10 Transcr_HoffmanL2_10 Transcr_Hoffman.extend.500L2_10 TSS_HoffmanL2_10 TSS_Hoffman.extend.500L2_10 UTR_3_UCSCL2_10 UTR_3_UCSC.extend.500L2_10 UTR_5_UCSCL2_10 UTR_5_UCSC.extend.500L2_10 WeakEnhancer_HoffmanL2_10 WeakEnhancer_Hoffman.extend.500L2_10 Observed scale h2: -1.1140e-02 2.8696e-03 1.9514e-02 -1.9888e-02 -1.9388e-02 9.4821e-03 1.0371e-02 -1.9996e-04 1.1755e-02 8.1449e-03 -3.6340e-03 2.3269e-02 2.8469e-03 -7.8512e-03 5.3765e-03 -2.5410e-02 -4.3140e-02 1.5348e-01 1.2243e-02 8.2591e-02 -3.7034e-02 1.1638e-02 3.9559e-03 -2.9589e-02 2.3772e-02 7.9015e-03 9.8916e-02 1.1840e-01 -1.6348e-01 -3.3068e-02 3.2873e-02 -4.7582e-02 -3.0708e-02 -8.2813e-02 -4.5125e-03 7.4176e-02 -6.2843e-02 1.0166e-02 -4.4358e-02 6.1990e-02 2.2052e-01 -2.5130e-01 7.9834e-03 -2.3422e-04 -3.4797e-02 2.1252e-02 7.5561e-02 -2.1303e-02 1.2079e-01 -1.1295e-01 9.7748e-03 -9.9526e-02 8.6393e-02 -1.1087e-01 3.1381e-03 -1.3834e-02 1.9031e-02 -3.6290e-02 -7.6089e-03 7.3197e-03 2.2923e-03 8.2349e-03 Observed scale h2 SE: 0.0097 0.009 0.0217 0.0165 0.0207 0.0184 0.0098 0.0077 0.0078 0.0108 0.0154 0.0185 0.0137 0.0353 0.0121 0.0186 0.0385 0.082 0.0513 0.0752 0.1061 0.0072 0.0109 0.0221 0.0303 0.0421 0.0602 0.1635 0.1727 0.0874 0.0923 0.0424 0.0993 0.1074 0.0208 0.0449 0.0531 0.0182 0.0448 0.0581 0.1357 0.1393 0.0071 0.0124 0.0347 0.0395 0.0586 0.0754 0.2296 0.2305 0.0375 0.0592 0.0515 0.0854 0.0138 0.0182 0.012 0.0143 0.0059 0.0125 0.0138 0.0239 Proportion of SNPs: 0.0025 0.0018 0.0036 0.0029 0.0035 0.0034 0.0021 0.0019 0.0019 0.0024 0.0027 0.0085 0.0042 0.0368 0.0022 0.0063 0.0152 0.0508 0.0137 0.0203 0.0493 0.0005 0.0018 0.0044 0.0086 0.0106 0.0297 0.0369 0.0394 0.0264 0.0319 0.0188 0.044 0.0575 0.0043 0.0134 0.0235 0.0042 0.0133 0.0224 0.035 0.0365 0.0008 0.003 0.0047 0.0056 0.0351 0.0561 0.016 0.0163 0.0138 0.0326 0.0294 0.0625 0.0017 0.0031 0.0018 0.0035 0.0007 0.0031 0.0023 0.0087 Proportion of h2g: -8.7952e-01 2.2656e-01 1.5407e+00 -1.5702e+00 -1.5308e+00 7.4864e-01 8.1882e-01 -1.5787e-02 9.2805e-01 6.4306e-01 -2.8692e-01 1.8372e+00 2.2477e-01 -6.1987e-01 4.2449e-01 -2.0062e+00 -3.4060e+00 1.2118e+01 9.6663e-01 6.5208e+00 -2.9239e+00 9.1881e-01 3.1233e-01 -2.3361e+00 1.8768e+00 6.2384e-01 7.8097e+00 9.3478e+00 -1.2907e+01 -2.6108e+00 2.5954e+00 -3.7567e+00 -2.4245e+00 -6.5383e+00 -3.5627e-01 5.8564e+00 -4.9616e+00 8.0262e-01 -3.5022e+00 4.8943e+00 1.7411e+01 -1.9841e+01 6.3031e-01 -1.8492e-02 -2.7473e+00 1.6779e+00 5.9657e+00 -1.6819e+00 9.5370e+00 -8.9176e+00 7.7175e-01 -7.8578e+00 6.8209e+00 -8.7538e+00 2.4776e-01 -1.0922e+00 1.5026e+00 -2.8652e+00 -6.0074e-01 5.7791e-01 1.8099e-01 6.5017e-01 Enrichment: -354.8941 125.4251 431.0764 -542.4178 -437.479 217.6542 395.8507 -8.1046 486.659 264.8367 -106.9417 215.0758 54.152 -16.8572 189.9499 -317.5343 -224.7307 238.3342 70.657 321.6991 -59.3459 2038.1524 169.3208 -528.0819 218.4244 59.0209 263.3467 253.2099 -327.6609 -98.9078 81.3445 -199.9036 -55.0528 -113.7103 -82.7486 436.6913 -211.0946 192.5995 -263.5375 218.7525 497.2064 -542.9375 759.9285 -6.1459 -590.6109 300.7862 169.9006 -29.9553 595.4353 -548.5177 55.9285 -241.3693 231.7269 -139.9886 145.8279 -348.4518 838.1112 -810.9449 -804.0632 186.2128 77.1948 75.0303 Coefficients: -3.4445e-07 1.2173e-07 4.1839e-07 -5.2645e-07 -4.2460e-07 2.1125e-07 3.8420e-07 -7.8661e-09 4.7234e-07 2.5704e-07 -1.0379e-07 2.0875e-07 5.2558e-08 -1.6361e-08 1.8436e-07 -3.0819e-07 -2.1812e-07 2.3132e-07 6.8577e-08 3.1223e-07 -5.7599e-08 1.9782e-06 1.6434e-07 -5.1254e-07 2.1200e-07 5.7284e-08 2.5560e-07 2.4576e-07 -3.1802e-07 -9.5997e-08 7.8950e-08 -1.9402e-07 -5.3433e-08 -1.1036e-07 -8.0313e-08 4.2384e-07 -2.0488e-07 1.8693e-07 -2.5578e-07 2.1231e-07 4.8257e-07 -5.2696e-07 7.3756e-07 -5.9650e-09 -5.7323e-07 2.9193e-07 1.6490e-07 -2.9074e-08 5.7791e-07 -5.3237e-07 5.4282e-08 -2.3427e-07 2.2491e-07 -1.3587e-07 1.4154e-07 -3.3820e-07 8.1344e-07 -7.8708e-07 -7.8040e-07 1.8073e-07 7.4923e-08 7.2822e-08 Coefficient SE: 2.9977e-07 3.8099e-07 4.6575e-07 4.3697e-07 4.5417e-07 4.1049e-07 3.6479e-07 3.0155e-07 3.1389e-07 3.3947e-07 4.3935e-07 1.6629e-07 2.5297e-07 7.3507e-08 4.1422e-07 2.2521e-07 1.9451e-07 1.2355e-07 2.8755e-07 2.8445e-07 1.6504e-07 1.2165e-06 4.5406e-07 3.8205e-07 2.6994e-07 3.0492e-07 1.5564e-07 3.3936e-07 3.3603e-07 2.5383e-07 2.2180e-07 1.7286e-07 1.7282e-07 1.4318e-07 3.7032e-07 2.5661e-07 1.7324e-07 3.3403e-07 2.5812e-07 1.9897e-07 2.9703e-07 2.9212e-07 6.6035e-07 3.1697e-07 5.7210e-07 5.4282e-07 1.2778e-07 1.0289e-07 1.0984e-06 1.0866e-06 2.0826e-07 1.3925e-07 1.3403e-07 1.0462e-07 6.2329e-07 4.4608e-07 5.1265e-07 3.1007e-07 6.0186e-07 3.0977e-07 4.5170e-07 2.1103e-07 Lambda GC: 1.0375 Mean Chi^2: 1.0252 Intercept: 1.0188 (0.0068) Ratio: 0.7457 (0.2699) Analysis finished at Sat Jun 22 17:19:04 2024 Total time elapsed: 8.0m:16.28s