********************************************************************* * 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/Glaucoma-Choquet_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.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.Glaucoma-Choquet_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 01:54:48 2024 Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/Glaucoma-Choquet_2018.sumstats.gz ... Read summary statistics for 1195704 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, 1183089 SNPs remain. After merging with regression SNP LD, 1183089 SNPs remain. Removed 54 SNPs with chi^2 > 80 (1183035 SNPs remain) Total Observed scale h2: 5462.5099 (470.5643) 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: 353.1176 -13.4251 403.5628 293.7175 -98.478 -141.4764 54.5455 42.4555 -53.0572 574.6501 -2020.1896 -307.1238 -686.5692 1200.9194 1290.9127 544.963 -1463.822 734.1997 545.0489 650.8152 1656.3815 14.5237 47.2445 -82.7161 131.3806 -148.6047 -83.7706 -1676.1835 -5697.6828 6046.2317 178.8877 353.4456 -346.4346 1620.4976 -823.4172 -217.574 486.2838 966.0971 138.4147 2005.1855 -369.4453 4857.4292 -4628.6258 251.3604 -508.425 -230.4721 416.6109 507.522 -1930.2774 1158.8504 -534.1832 -104.3603 183.3365 -952.6304 1541.2184 -81.6959 -422.6765 544.0334 -565.8294 106.9474 -149.2054 466.4685 -566.3976 Observed scale h2 SE: 270.8344 228.6484 458.6579 428.8999 458.9329 421.6214 230.5134 192.4903 251.2905 366.0304 712.9026 292.4288 450.5832 283.4031 818.448 240.6863 402.7474 839.8707 1683.0981 1035.23 1426.0003 2150.8511 122.6844 214.242 476.0662 650.9699 879.577 1162.0213 3028.944 3235.7272 1486.2969 1621.5035 872.997 1944.2984 2231.7806 375.4547 825.3117 1132.9285 440.566 911.6588 1092.7182 2233.1786 2320.4749 158.0241 255.9979 745.0536 770.6751 1557.982 1712.7471 4394.3802 4356.5324 780.0224 1272.0688 1110.8923 1714.3225 293.6211 385.4676 290.7131 350.2069 132.0294 263.2649 287.3901 487.9618 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: 0.0646 -0.0025 0.0739 0.0538 -0.018 -0.0259 0.01 0.0078 -0.0097 0.1052 -0.3698 -0.0562 -0.1257 0.2198 0.2363 0.0998 -0.268 0.1344 0.0998 0.1191 0.3032 0.0027 0.0086 -0.0151 0.0241 -0.0272 -0.0153 -0.3069 -1.0431 1.1069 0.0327 0.0647 -0.0634 0.2967 -0.1507 -0.0398 0.089 0.1769 0.0253 0.3671 -0.0676 0.8892 -0.8473 0.046 -0.0931 -0.0422 0.0763 0.0929 -0.3534 0.2121 -0.0978 -0.0191 0.0336 -0.1744 0.2821 -0.015 -0.0774 0.0996 -0.1036 0.0196 -0.0273 0.0854 -0.1037 Enrichment: 2.6367e+01 -1.3753e+00 2.0895e+01 1.8775e+01 -5.2081e+00 -7.6114e+00 4.8796e+00 4.0332e+00 -5.1485e+00 4.3794e+01 -3.4538e+01 -2.1183e+01 -1.4874e+01 5.3540e+01 6.4962e+00 4.5126e+01 -4.2873e+01 8.9642e+00 1.9837e+00 8.8031e+00 1.5121e+01 5.4549e-02 1.9393e+01 -8.2979e+00 5.4957e+00 -3.2003e+00 -1.4666e+00 -1.0459e+01 -2.8560e+01 2.8403e+01 1.2540e+00 2.0499e+00 -3.4113e+00 6.8091e+00 -2.6499e+00 -9.3513e+00 6.7100e+00 7.6060e+00 6.1462e+00 2.7922e+01 -3.0556e+00 2.5669e+01 -2.3438e+01 5.6079e+01 -3.1268e+01 -9.1684e+00 1.3820e+01 2.6747e+00 -6.3616e+00 1.3389e+01 -6.0802e+00 -1.3995e+00 1.0421e+00 -5.9888e+00 4.5608e+00 -8.8979e+00 -2.4954e+01 5.6153e+01 -2.9635e+01 2.6488e+01 -8.8965e+00 3.6817e+01 -1.2095e+01 Coefficients: 1.0919e-02 -5.6951e-04 8.6525e-03 7.7748e-03 -2.1567e-03 -3.1519e-03 2.0207e-03 1.6702e-03 -2.1320e-03 1.8135e-02 -1.4302e-02 -8.7720e-03 -6.1592e-03 2.2171e-02 2.6901e-03 1.8687e-02 -1.7754e-02 3.7121e-03 8.2148e-04 3.6454e-03 6.2619e-03 2.2589e-05 8.0307e-03 -3.4362e-03 2.2758e-03 -1.3253e-03 -6.0731e-04 -4.3312e-03 -1.1827e-02 1.1762e-02 5.1931e-04 8.4887e-04 -1.4126e-03 2.8197e-03 -1.0974e-03 -3.8724e-03 2.7786e-03 3.1497e-03 2.5452e-03 1.1562e-02 -1.2653e-03 1.0630e-02 -9.7059e-03 2.3223e-02 -1.2948e-02 -3.7967e-03 5.7229e-03 1.1076e-03 -2.6344e-03 5.5443e-03 -2.5178e-03 -5.7954e-04 4.3154e-04 -2.4800e-03 1.8887e-03 -3.6846e-03 -1.0333e-02 2.3253e-02 -1.2272e-02 1.0969e-02 -3.6841e-03 1.5246e-02 -5.0087e-03 Coefficient SE: 0.0084 0.0097 0.0098 0.0114 0.0101 0.0094 0.0085 0.0076 0.0101 0.0116 0.005 0.0084 0.004 0.0052 0.0017 0.0083 0.0049 0.0042 0.0025 0.0058 0.0054 0.0033 0.0209 0.0089 0.0082 0.0058 0.0064 0.003 0.0063 0.0063 0.0043 0.0039 0.0036 0.0034 0.003 0.0067 0.0047 0.0037 0.0081 0.0053 0.0037 0.0049 0.0049 0.0146 0.0065 0.0123 0.0106 0.0034 0.0023 0.021 0.0205 0.0043 0.003 0.0029 0.0021 0.0132 0.0094 0.0124 0.0076 0.0135 0.0065 0.0094 0.0043 Lambda GC: 1.1491 Mean Chi^2: 1.2158 Intercept: 1.0158 (0.0102) Ratio: 0.0731 (0.0472) Analysis finished at Mon Jun 24 01:58:04 2024 Total time elapsed: 3.0m:15.72s