********************************************************************* * 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/OpioidDep-Cheng_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.OpioidDep-Cheng_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 14:59:44 2024 Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/OpioidDep-Cheng_2018.sumstats.gz ... Read summary statistics for 1174403 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, 1166644 SNPs remain. After merging with regression SNP LD, 1166644 SNPs remain. Removed 0 SNPs with chi^2 > 80 (1166644 SNPs remain) Total Observed scale h2: 0.025 (0.0665) 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: -0.0258 0.0075 -0.0455 0.0099 0.0914 -0.0347 0.0361 -0.0194 0.011 -0.074 -0.0557 0.0205 -0.0281 0.0473 -0.0176 0.0049 0.0419 0.2525 -0.6417 -0.2625 0.0578 0.4315 0.0235 0.0067 -0.0339 -0.0039 0.0303 0.0465 -0.3462 0.0808 -0.6328 0.6928 0.1521 -0.0075 0.2727 -0.0356 -0.0132 0.1306 -0.0468 -0.0401 0.0467 -0.3672 0.3115 0.0404 -0.0523 -0.0724 0.0967 -0.3262 0.565 -0.2194 0.2913 0.087 -0.2637 0.2277 -0.4367 -0.0468 0.1123 -0.0374 -0.0162 -0.0336 0.0291 -0.0405 0.0462 Observed scale h2 SE: 0.0359 0.0312 0.0811 0.0619 0.082 0.053 0.0381 0.0275 0.027 0.0349 0.123 0.0519 0.0741 0.0518 0.1353 0.0466 0.0684 0.129 0.3018 0.1658 0.2142 0.3385 0.0201 0.0349 0.0783 0.1164 0.1271 0.1957 0.5204 0.5668 0.3072 0.3394 0.1561 0.3735 0.4288 0.0554 0.1338 0.1867 0.0587 0.139 0.1796 0.3085 0.3227 0.0247 0.0406 0.1233 0.1222 0.1934 0.2628 0.8826 0.8912 0.118 0.2054 0.1594 0.295 0.0473 0.0694 0.0415 0.0528 0.0235 0.049 0.0456 0.0847 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: -1.0322 0.299 -1.8232 0.3976 3.6644 -1.3903 1.4474 -0.7785 0.4411 -2.9661 -2.2318 0.8232 -1.1272 1.8943 -0.7038 0.1975 1.6793 10.1169 -25.7157 -10.5199 2.3167 17.289 0.9421 0.2704 -1.3575 -0.1559 1.2161 1.8624 -13.871 3.2375 -25.3564 27.7604 6.0931 -0.2988 10.9261 -1.4251 -0.5304 5.2339 -1.875 -1.6055 1.872 -14.7127 12.4829 1.6184 -2.0938 -2.902 3.8733 -13.0708 22.6398 -8.7925 11.6745 3.4872 -10.5685 9.1242 -17.5001 -1.8769 4.4991 -1.4969 -0.6473 -1.3447 1.1649 -1.6237 1.8497 Enrichment: -422.6203 183.8852 -428.3937 122.7923 894.559 -451.7204 501.6437 -405.5153 234.7045 -1239.5183 -180.798 311.3365 -133.9051 463.0896 -19.4212 89.6932 269.692 677.3352 -513.2222 -780.2738 115.974 356.0701 2120.6289 148.7671 -311.3714 -18.4154 116.7416 63.7262 -381.2577 83.3942 -974.7133 882.8599 328.9926 -6.8857 192.8133 -335.872 -40.1284 225.9545 -456.5509 -122.5891 84.8985 -426.3356 346.6144 1979.9248 -706.1003 -633.0337 704.5505 -377.7249 409.1443 -557.0297 728.6556 256.4324 -329.4088 314.5337 -283.9724 -1120.9708 1456.49 -847.2017 -185.8981 -1826.236 380.8749 -702.7444 216.6022 Coefficients: -7.9646e-07 3.4655e-07 -8.0734e-07 2.3141e-07 1.6859e-06 -8.5130e-07 9.4539e-07 -7.6423e-07 4.4232e-07 -2.3360e-06 -3.4073e-07 5.8674e-07 -2.5235e-07 8.7273e-07 -3.6601e-08 1.6903e-07 5.0826e-07 1.2765e-06 -9.6721e-07 -1.4705e-06 2.1856e-07 6.7104e-07 3.9965e-06 2.8036e-07 -5.8680e-07 -3.4705e-08 2.2001e-07 1.2010e-07 -7.1851e-07 1.5716e-07 -1.8369e-06 1.6638e-06 6.2001e-07 -1.2977e-08 3.6337e-07 -6.3298e-07 -7.5625e-08 4.2583e-07 -8.6041e-07 -2.3103e-07 1.6000e-07 -8.0346e-07 6.5322e-07 3.7313e-06 -1.3307e-06 -1.1930e-06 1.3278e-06 -7.1185e-07 7.7106e-07 -1.0498e-06 1.3732e-06 4.8327e-07 -6.2080e-07 5.9276e-07 -5.3517e-07 -2.1126e-06 2.7449e-06 -1.5966e-06 -3.5034e-07 -3.4417e-06 7.1779e-07 -1.3244e-06 4.0820e-07 Coefficient SE: 1.1106e-06 1.4509e-06 1.4388e-06 1.4446e-06 1.5108e-06 1.2996e-06 9.9707e-07 1.0808e-06 1.0843e-06 1.1003e-06 7.5249e-07 1.4812e-06 6.6513e-07 9.5571e-07 2.8185e-07 1.5994e-06 8.2976e-07 6.5246e-07 4.5489e-07 9.2856e-07 8.0980e-07 5.2653e-07 3.4228e-06 1.4497e-06 1.3569e-06 1.0379e-06 9.2175e-07 5.0557e-07 1.0801e-06 1.1026e-06 8.9186e-07 8.1514e-07 6.3640e-07 6.4992e-07 5.7148e-07 9.8530e-07 7.6425e-07 6.0875e-07 1.0793e-06 8.0129e-07 6.1521e-07 6.7507e-07 6.7668e-07 2.2840e-06 1.0345e-06 2.0307e-06 1.6788e-06 4.2197e-07 3.5866e-07 4.2227e-06 4.2006e-06 6.5542e-07 4.8340e-07 4.1485e-07 3.6146e-07 2.1324e-06 1.6974e-06 1.7736e-06 1.1448e-06 2.4143e-06 1.2110e-06 1.4890e-06 7.4945e-07 Lambda GC: 1.0436 Mean Chi^2: 1.0324 Intercept: 1.0288 (0.0062) Ratio: 0.8885 (0.191) Analysis finished at Mon Jun 24 15:02:18 2024 Total time elapsed: 2.0m:33.39s