********************************************************************* * 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/OD_vs_OE_AFR-Polimanti_2020.sumstats.gz \ --ref-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.AFR. \ --out /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/conditional/Human_Striatum_snATAC.conditional.OD_vs_OE_AFR-Polimanti_2020.AFR \ --w-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/weights/1000G.AFR.weights.hm3_noMHC. \ --print-coefficients Beginning analysis at Sat Jun 22 17:10:49 2024 Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/OD_vs_OE_AFR-Polimanti_2020.sumstats.gz ... Read summary statistics for 1000168 SNPs. Reading reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.AFR.[1-22] ... (ldscore_fromlist) Read reference panel LD Scores for 1192221 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.AFR.weights.hm3_noMHC.[1-22] ... (ldscore_fromlist) Read regression weight LD Scores for 1192221 SNPs. After merging with reference panel LD, 996140 SNPs remain. After merging with regression SNP LD, 996140 SNPs remain. Removed 0 SNPs with chi^2 > 80 (996140 SNPs remain) Total Observed scale h2: 0.3389 (0.2892) 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: 0.198 0.0594 0.2929 0.0738 -0.5932 -0.0249 -0.036 0.0323 -0.1927 0.0619 0.0313 0.1613 -0.3237 0.1918 0.1061 -0.0243 -0.0677 0.0343 -0.3703 1.0594 -0.4692 0.011 -0.0403 -0.2027 -0.0718 0.2982 -0.1042 -0.5708 0.5052 -0.551 1.7601 0.172 3.1033 -3.7225 -0.0469 -0.4749 0.7205 -0.1412 0.2606 -0.2225 1.7672 -1.5221 -0.0467 0.1561 0.2299 -0.24 0.0387 -0.3141 7.7844 -8.1285 -0.2197 -0.1936 -1.0607 1.5612 -0.3016 0.4387 0.1278 -0.1415 0.0813 -0.1199 -0.1482 -0.2928 Observed scale h2 SE: 0.137 0.1033 0.2201 0.1965 0.2188 0.2061 0.1285 0.1052 0.0998 0.1225 0.1881 0.268 0.1432 0.4373 0.1516 0.2299 0.4067 1.1582 0.5448 0.7514 1.1971 0.0583 0.102 0.2254 0.3441 0.4455 0.7187 1.8161 1.9143 1.0202 1.1812 0.4861 1.0573 1.2789 0.2129 0.5011 0.6438 0.2167 0.5124 0.6569 2.212 2.2822 0.0861 0.152 0.421 0.4221 0.7326 0.8876 2.3776 2.3925 0.4314 0.7063 0.5439 1.0699 0.1589 0.2366 0.1473 0.1654 0.0802 0.1447 0.153 0.31 Proportion of SNPs: 0.0025 0.0018 0.0036 0.0029 0.0035 0.0034 0.0021 0.0019 0.0019 0.0024 0.0026 0.0085 0.004 0.0366 0.0022 0.0063 0.0151 0.0509 0.0136 0.0202 0.0493 0.0004 0.0018 0.0044 0.0086 0.0105 0.0297 0.037 0.0395 0.0264 0.0319 0.0188 0.0441 0.0576 0.0043 0.0134 0.0235 0.0041 0.0132 0.0223 0.035 0.0365 0.0008 0.003 0.0046 0.0056 0.0353 0.0565 0.016 0.0162 0.0138 0.0326 0.0295 0.0627 0.0017 0.0031 0.0018 0.0035 0.0007 0.0031 0.0023 0.0087 Proportion of h2g: 0.5843 0.1754 0.8641 0.2177 -1.7503 -0.0734 -0.1062 0.0952 -0.5687 0.1827 0.0923 0.476 -0.9551 0.5659 0.3131 -0.0717 -0.1998 0.1013 -1.0925 3.1257 -1.3843 0.0325 -0.1188 -0.5981 -0.2118 0.8798 -0.3073 -1.6841 1.4905 -1.6257 5.1933 0.5076 9.1566 -10.9835 -0.1384 -1.4012 2.126 -0.4166 0.769 -0.6565 5.2144 -4.491 -0.1379 0.4606 0.6783 -0.7081 0.1142 -0.9268 22.9687 -23.9838 -0.6481 -0.5711 -3.1296 4.6064 -0.89 1.2943 0.3772 -0.4175 0.2399 -0.3537 -0.4371 -0.864 Enrichment: 236.7303 97.6992 243.077 75.564 -502.579 -21.3951 -51.7635 49.154 -298.8853 75.632 35.0139 56.0561 -238.8248 15.4418 139.486 -11.3041 -13.1997 1.989 -80.0652 154.3568 -28.062 72.7463 -64.8223 -135.6898 -24.6787 83.6062 -10.364 -45.5597 37.7801 -61.6144 162.7796 27.0531 207.8166 -190.8091 -32.2089 -104.7424 90.5382 -100.6585 58.0963 -29.4105 148.8925 -123.0055 -166.3533 153.4586 146.0725 -127.171 3.2347 -16.4112 1435.5365 -1476.4494 -47.0614 -17.524 -106.2638 73.483 -526.2823 414.0011 211.1131 -118.2593 328.437 -114.7356 -187.4664 -99.7384 Coefficients: 6.4294e-06 2.6534e-06 6.6018e-06 2.0523e-06 -1.3650e-05 -5.8108e-07 -1.4059e-06 1.3350e-06 -8.1175e-06 2.0541e-06 9.5095e-07 1.5224e-06 -6.4863e-06 4.1939e-07 3.7883e-06 -3.0701e-07 -3.5849e-07 5.4021e-08 -2.1745e-06 4.1922e-06 -7.6214e-07 1.9757e-06 -1.7605e-06 -3.6852e-06 -6.7026e-07 2.2707e-06 -2.8148e-07 -1.2374e-06 1.0261e-06 -1.6734e-06 4.4210e-06 7.3474e-07 5.6442e-06 -5.1822e-06 -8.7477e-07 -2.8447e-06 2.4590e-06 -2.7338e-06 1.5779e-06 -7.9877e-07 4.0438e-06 -3.3407e-06 -4.5180e-06 4.1678e-06 3.9672e-06 -3.4539e-06 8.7852e-08 -4.4572e-07 3.8988e-05 -4.0099e-05 -1.2782e-06 -4.7594e-07 -2.8861e-06 1.9957e-06 -1.4293e-05 1.1244e-05 5.7337e-06 -3.2118e-06 8.9201e-06 -3.1161e-06 -5.0915e-06 -2.7088e-06 Coefficient SE: 4.4478e-06 4.6101e-06 4.9614e-06 5.4666e-06 5.0338e-06 4.8148e-06 5.0178e-06 4.3502e-06 4.2025e-06 4.0650e-06 5.7201e-06 2.5289e-06 2.8690e-06 9.5622e-07 5.4110e-06 2.9027e-06 2.1535e-06 1.8220e-06 3.1993e-06 2.9734e-06 1.9447e-06 1.0468e-05 4.4589e-06 4.0983e-06 3.2136e-06 3.3927e-06 1.9421e-06 3.9372e-06 3.8883e-06 3.0985e-06 2.9669e-06 2.0760e-06 1.9230e-06 1.7804e-06 3.9717e-06 3.0016e-06 2.1971e-06 4.1955e-06 3.1020e-06 2.3582e-06 5.0615e-06 5.0092e-06 8.3211e-06 4.0594e-06 7.2657e-06 6.0745e-06 1.6635e-06 1.2596e-06 1.1908e-05 1.1803e-05 2.5100e-06 1.7368e-06 1.4800e-06 1.3677e-06 7.5276e-06 6.0657e-06 6.6078e-06 3.7547e-06 8.8007e-06 3.7612e-06 5.2587e-06 2.8673e-06 Lambda GC: 1.0225 Mean Chi^2: 1.0205 Intercept: 1.0113 (0.0064) Ratio: 0.5514 (0.3107) Analysis finished at Sat Jun 22 17:19:02 2024 Total time elapsed: 8.0m:13.44s