********************************************************************* * 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_UX_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/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.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_UX_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 Mon Jun 24 01:58:07 2024 Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/OD_vs_UX_AFR-Polimanti_2020.sumstats.gz ... Read summary statistics for 978488 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/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.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, 975573 SNPs remain. After merging with regression SNP LD, 975573 SNPs remain. Removed 0 SNPs with chi^2 > 80 (975573 SNPs remain) Total Observed scale h2: -0.0719 (0.0987) 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: 0.0281 -0.0028 0.0173 -0.0287 0.0411 0.0388 0.0155 0.0102 0.0428 -0.027 -0.2284 -0.1863 0.1763 0.0276 -0.3203 -0.015 -0.0254 -0.1173 0.0077 -0.1839 0.1615 -0.3354 0.0158 0.0056 0.0135 0.0038 0.0703 0.19 0.7063 -0.7247 0.1149 0.2039 0.3557 0.3061 -0.105 -0.1549 -0.067 0.1633 0.0326 0.281 -0.4814 0.1712 -0.2145 -0.0247 0.0174 0.1302 -0.1152 -0.0606 0.0897 0.2369 -0.335 -0.0795 0.0464 -0.0448 0.2365 0.0209 -0.0474 0.0988 -0.0861 0.0504 -0.0401 -0.021 -0.1275 Observed scale h2 SE: 0.046 0.0398 0.09 0.0784 0.09 0.0722 0.0384 0.0355 0.0347 0.0442 0.1277 0.052 0.0893 0.051 0.167 0.0548 0.0731 0.1505 0.3271 0.1829 0.2604 0.3806 0.0205 0.0345 0.0797 0.1226 0.1427 0.2604 0.6088 0.6475 0.3043 0.3704 0.1752 0.3874 0.4571 0.0732 0.1732 0.2264 0.0673 0.1736 0.212 0.6984 0.7188 0.0298 0.0509 0.1354 0.1461 0.2618 0.3162 0.8316 0.845 0.1412 0.2452 0.1961 0.3726 0.0542 0.0769 0.0535 0.0605 0.028 0.0525 0.0526 0.0891 Proportion of SNPs: 0.0024 0.0018 0.0035 0.0029 0.0034 0.0034 0.002 0.0019 0.0019 0.0024 0.0107 0.0026 0.0084 0.004 0.0363 0.0022 0.0063 0.015 0.0504 0.0135 0.02 0.0488 0.0004 0.0018 0.0044 0.0085 0.0104 0.0293 0.0366 0.039 0.0261 0.0316 0.0186 0.0436 0.0569 0.0042 0.0132 0.0232 0.0041 0.0131 0.0221 0.0346 0.0361 0.0008 0.003 0.0046 0.0055 0.0349 0.0559 0.0158 0.0161 0.0136 0.0322 0.0291 0.062 0.0017 0.0031 0.0018 0.0035 0.0007 0.003 0.0023 0.0086 Proportion of h2g: -0.3907 0.039 -0.2404 0.3997 -0.5726 -0.5396 -0.2163 -0.1413 -0.5957 0.3764 3.1786 2.592 -2.4531 -0.3845 4.4571 0.2085 0.354 1.6328 -0.1077 2.5594 -2.2471 4.6676 -0.2202 -0.0777 -0.1883 -0.0524 -0.9782 -2.6441 -9.8296 10.0851 -1.5993 -2.8373 -4.9501 -4.2598 1.4605 2.156 0.9329 -2.2732 -0.4533 -3.9105 6.6996 -2.3827 2.9844 0.3444 -0.2415 -1.8121 1.6037 0.843 -1.248 -3.2967 4.6617 1.1058 -0.6462 0.6235 -3.2907 -0.2906 0.6594 -1.3744 1.1982 -0.7014 0.5583 0.2922 1.7739 Enrichment: -159.9828 21.9343 -68.3447 140.2394 -166.1731 -159.0103 -106.59 -73.7303 -316.4557 157.518 297.8729 994.1166 -292.0052 -97.1899 122.9402 93.8944 56.3791 109.0489 -2.138 189.5892 -112.1654 95.6399 -498.3385 -42.8392 -43.1848 -6.1694 -93.9618 -90.1256 -268.792 258.3838 -61.2689 -89.8908 -266.6621 -97.7237 25.6466 507.2905 70.4876 -97.8517 -110.7199 -298.6252 303.365 -68.7714 82.622 419.8248 -81.3233 -394.4352 291.1163 24.1439 -22.3375 -208.2654 290.069 81.1567 -20.0421 21.4001 -53.0609 -173.719 213.2112 -777.5991 343.0236 -970.4717 183.0603 126.6594 206.9787 Coefficients: 9.1142e-07 -1.2496e-07 3.8936e-07 -7.9894e-07 9.4668e-07 9.0588e-07 6.0724e-07 4.2004e-07 1.8028e-06 -8.9738e-07 -1.6970e-06 -5.6635e-06 1.6635e-06 5.5369e-07 -7.0039e-07 -5.3491e-07 -3.2119e-07 -6.2125e-07 1.2180e-08 -1.0801e-06 6.3900e-07 -5.4486e-07 2.8390e-06 2.4405e-07 2.4602e-07 3.5147e-08 5.3530e-07 5.1344e-07 1.5313e-06 -1.4720e-06 3.4905e-07 5.1211e-07 1.5192e-06 5.5673e-07 -1.4611e-07 -2.8900e-06 -4.0157e-07 5.5746e-07 6.3077e-07 1.7013e-06 -1.7283e-06 3.9179e-07 -4.7070e-07 -2.3917e-06 4.6330e-07 2.2471e-06 -1.6585e-06 -1.3755e-07 1.2726e-07 1.1865e-06 -1.6525e-06 -4.6235e-07 1.1418e-07 -1.2192e-07 3.0229e-07 9.8967e-07 -1.2147e-06 4.4300e-06 -1.9542e-06 5.5287e-06 -1.0429e-06 -7.2158e-07 -1.1792e-06 Coefficient SE: 1.4926e-06 1.7787e-06 2.0279e-06 2.1814e-06 2.0710e-06 1.6865e-06 1.4997e-06 1.4673e-06 1.4629e-06 1.4656e-06 9.4871e-07 1.5823e-06 8.4265e-07 1.0214e-06 3.6510e-07 1.9561e-06 9.2315e-07 7.9712e-07 5.1458e-07 1.0743e-06 1.0306e-06 6.1827e-07 3.6850e-06 1.5086e-06 1.4484e-06 1.1454e-06 1.0865e-06 7.0375e-07 1.3199e-06 1.3152e-06 9.2417e-07 9.3046e-07 7.4841e-07 7.0457e-07 6.3629e-07 1.3655e-06 1.0375e-06 7.7277e-07 1.3037e-06 1.0510e-06 7.6097e-07 1.5981e-06 1.5778e-06 2.8783e-06 1.3602e-06 2.3363e-06 2.1028e-06 5.9440e-07 4.4873e-07 4.1648e-06 4.1685e-06 8.2180e-07 6.0298e-07 5.3370e-07 4.7627e-07 2.5677e-06 1.9715e-06 2.3991e-06 1.3729e-06 3.0719e-06 1.3660e-06 1.8068e-06 8.2383e-07 Lambda GC: 1.0195 Mean Chi^2: 1.0202 Intercept: 1.0259 (0.0059) Ratio: 1.2833 (0.2911) Analysis finished at Mon Jun 24 02:01:20 2024 Total time elapsed: 3.0m:13.18s