********************************************************************* * 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/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.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 Mon Jun 24 01:55:11 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/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.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: 0.0102 (0.0178) 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.merged_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: -0.0048 0.0058 0.0273 -0.0199 -0.0121 0.0179 0.0138 0.0058 0.016 0.0133 -0.0687 -0.0032 0.0226 0.003 -0.0074 0.0034 -0.0243 -0.0428 0.1514 0.0094 0.0823 -0.0339 0.0118 0.0042 -0.0291 0.023 0.0053 0.108 0.1194 -0.1658 -0.0285 0.0333 -0.0409 -0.0273 -0.0869 -0.0055 0.0739 -0.0616 0.0104 -0.0465 0.0632 0.2349 -0.2629 0.008 -0.0024 -0.0356 0.0217 0.0777 -0.0221 0.1217 -0.1126 0.008 -0.0988 0.0857 -0.1096 -0.0006 -0.0126 0.0194 -0.0366 -0.0077 0.0066 0.0029 0.0098 Observed scale h2 SE: 0.0104 0.0092 0.022 0.0165 0.0208 0.0188 0.01 0.0083 0.0081 0.011 0.0329 0.0154 0.0185 0.0137 0.0352 0.0121 0.0186 0.0383 0.0818 0.0513 0.0751 0.1059 0.0072 0.0109 0.0221 0.0303 0.0421 0.0605 0.1632 0.1725 0.0876 0.0924 0.0424 0.0992 0.1074 0.0207 0.0448 0.0532 0.0182 0.0448 0.058 0.1376 0.141 0.0071 0.0126 0.0347 0.0395 0.0585 0.0753 0.2294 0.2304 0.0375 0.0591 0.0514 0.0852 0.0138 0.0182 0.012 0.0143 0.0058 0.0126 0.0138 0.024 Proportion of SNPs: 0.0025 0.0018 0.0035 0.0029 0.0035 0.0034 0.002 0.0019 0.0019 0.0024 0.0107 0.0027 0.0085 0.0041 0.0364 0.0022 0.0063 0.015 0.0503 0.0135 0.0201 0.0487 0.0004 0.0018 0.0044 0.0085 0.0105 0.0293 0.0365 0.039 0.0261 0.0316 0.0186 0.0436 0.0569 0.0043 0.0133 0.0233 0.0041 0.0131 0.0221 0.0346 0.0362 0.0008 0.003 0.0046 0.0055 0.0347 0.0555 0.0158 0.0161 0.0137 0.0322 0.0291 0.0619 0.0017 0.0031 0.0018 0.0035 0.0007 0.0031 0.0023 0.0086 Proportion of h2g: -0.476 0.5733 2.6886 -1.9591 -1.1927 1.7569 1.3528 0.5705 1.5724 1.3122 -6.762 -0.3166 2.2188 0.2926 -0.7261 0.3331 -2.3911 -4.206 14.8949 0.9259 8.0943 -3.3325 1.1653 0.4113 -2.8614 2.2616 0.5204 10.6197 11.7466 -16.3047 -2.8015 3.2785 -4.0237 -2.6803 -8.5513 -0.5426 7.2705 -6.0583 1.0256 -4.5736 6.2115 23.1032 -25.8536 0.791 -0.2355 -3.5021 2.1341 7.6394 -2.1744 11.9719 -11.0775 0.7907 -9.7202 8.4259 -10.7835 -0.0639 -1.2358 1.9082 -3.6009 -0.761 0.6495 0.2901 0.9666 Enrichment: -194.1583 320.8292 760.3853 -684.0593 -344.545 516.3136 661.0739 296.0615 833.4984 546.2431 -631.4982 -119.2938 262.5706 71.2645 -19.9591 150.6477 -382.5464 -280.5199 296.129 68.4132 403.6521 -68.3706 2612.7886 225.3684 -653.8269 266.0559 49.7702 361.9786 321.6326 -418.3901 -107.2802 103.8669 -216.425 -61.5209 -150.3277 -127.3875 548.0051 -260.5457 248.7766 -347.8856 280.6307 666.9109 -715.1343 963.9942 -79.103 -761.0268 386.7053 219.9202 -39.1447 755.5482 -688.7508 57.9245 -301.8086 289.3528 -174.3127 -38.0201 -398.5237 1075.9031 -1030.2191 -1029.5934 211.5431 125.0567 112.7517 Coefficients: -1.4965e-07 2.4728e-07 5.8606e-07 -5.2723e-07 -2.6556e-07 3.9794e-07 5.0952e-07 2.2819e-07 6.4241e-07 4.2101e-07 -4.8672e-07 -9.1945e-08 2.0237e-07 5.4926e-08 -1.5383e-08 1.1611e-07 -2.9484e-07 -2.1621e-07 2.2824e-07 5.2729e-08 3.1111e-07 -5.2696e-08 2.0138e-06 1.7370e-07 -5.0393e-07 2.0506e-07 3.8360e-08 2.7899e-07 2.4790e-07 -3.2247e-07 -8.2685e-08 8.0055e-08 -1.6681e-07 -4.7417e-08 -1.1586e-07 -9.8183e-08 4.2237e-07 -2.0081e-07 1.9174e-07 -2.6813e-07 2.1629e-07 5.1402e-07 -5.5118e-07 7.4299e-07 -6.0968e-08 -5.8655e-07 2.9805e-07 1.6950e-07 -3.0170e-08 5.8233e-07 -5.3085e-07 4.4645e-08 -2.3262e-07 2.2302e-07 -1.3435e-07 -2.9304e-08 -3.0716e-07 8.2924e-07 -7.9403e-07 -7.9355e-07 1.6305e-07 9.6386e-08 8.6902e-08 Coefficient SE: 3.2094e-07 3.9189e-07 4.7191e-07 4.3639e-07 4.5555e-07 4.1932e-07 3.6954e-07 3.2798e-07 3.2406e-07 3.4817e-07 2.3293e-07 4.3886e-07 1.6587e-07 2.5284e-07 7.3396e-08 4.1369e-07 2.2617e-07 1.9386e-07 1.2331e-07 2.8716e-07 2.8402e-07 1.6470e-07 1.2172e-06 4.5417e-07 3.8289e-07 2.7013e-07 3.0540e-07 1.5628e-07 3.3880e-07 3.3555e-07 2.5439e-07 2.2186e-07 1.7270e-07 1.7263e-07 1.4312e-07 3.6853e-07 2.5573e-07 1.7333e-07 3.3383e-07 2.5820e-07 1.9855e-07 3.0109e-07 2.9569e-07 6.6010e-07 3.2118e-07 5.7184e-07 5.4316e-07 1.2770e-07 1.0282e-07 1.0974e-06 1.0859e-06 2.0808e-07 1.3914e-07 1.3391e-07 1.0440e-07 6.2313e-07 4.4539e-07 5.1383e-07 3.1073e-07 5.9969e-07 3.1045e-07 4.5040e-07 2.1218e-07 Lambda GC: 1.0375 Mean Chi^2: 1.0252 Intercept: 1.0195 (0.0068) Ratio: 0.776 (0.2689) Analysis finished at Mon Jun 24 02:12:13 2024 Total time elapsed: 17.0m:2.3s