********************************************************************* * 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/PD-Nalls_2019.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/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.PD-Nalls_2019.EUR \ --w-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC. \ --print-coefficients Beginning analysis at Sat Jun 22 17:10:44 2024 Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/PD-Nalls_2019.sumstats.gz ... Read summary statistics for 1132921 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/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, 1126254 SNPs remain. After merging with regression SNP LD, 1126254 SNPs remain. Removed 0 SNPs with chi^2 > 482.73 (1126254 SNPs remain) Total Observed scale h2: 0.0172 (0.0019) 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: -0.0004 -0.0006 0.0009 0.0006 -0.0021 0.0031 -0.0007 0.0009 0.0003 0.0011 -0.0014 -0.0004 0.0006 0.001 0.0004 -0.0015 -0.0037 -0.0086 0.0039 -0.0043 0.0174 0.0003 -0.0001 0.0032 -0.0028 0.0027 -0.0114 -0.0052 0.0158 0.0039 -0.0094 0.0071 -0.0095 0.0106 -0.0012 0.0015 0.0055 0.0012 -0.0041 0.0033 -0.0283 0.0301 0.0003 -0.0014 -0.01 0.0104 0.005 -0.0048 0.0023 -0.0056 -0.0036 -0.0013 0.0054 -0.0042 0.001 0.0003 0.0008 0.0006 -0.0007 0.0019 -0.0006 0.0012 Observed scale h2 SE: 0.0011 0.0009 0.0018 0.0015 0.0019 0.002 0.0008 0.0009 0.0009 0.001 0.0014 0.002 0.0012 0.0036 0.0013 0.0021 0.0033 0.0082 0.0037 0.0046 0.0093 0.0004 0.0008 0.0025 0.0026 0.003 0.005 0.0161 0.0166 0.0073 0.0091 0.0035 0.0091 0.01 0.0018 0.0036 0.0058 0.0015 0.0031 0.0048 0.0126 0.0132 0.0007 0.0011 0.0039 0.004 0.0061 0.0081 0.0228 0.0231 0.0035 0.0069 0.0034 0.0067 0.0014 0.0017 0.0013 0.0014 0.0006 0.0013 0.0012 0.0022 Proportion of SNPs: 0.0025 0.0018 0.0036 0.0029 0.0035 0.0034 0.0021 0.0019 0.0019 0.0024 0.0027 0.0085 0.0042 0.0368 0.0022 0.0063 0.0152 0.0508 0.0137 0.0203 0.0493 0.0005 0.0018 0.0044 0.0086 0.0106 0.0297 0.0369 0.0394 0.0264 0.0319 0.0188 0.044 0.0575 0.0043 0.0134 0.0235 0.0042 0.0133 0.0224 0.035 0.0365 0.0008 0.003 0.0047 0.0056 0.0351 0.0561 0.016 0.0163 0.0138 0.0326 0.0294 0.0625 0.0017 0.0031 0.0018 0.0035 0.0007 0.0031 0.0023 0.0087 Proportion of h2g: -0.0208 -0.0323 0.0548 0.0336 -0.1243 0.1782 -0.0404 0.0548 0.0195 0.0656 -0.0804 -0.0254 0.0326 0.0609 0.0229 -0.0877 -0.2152 -0.5008 0.2258 -0.2519 1.0128 0.0188 -0.0064 0.1863 -0.1651 0.159 -0.6634 -0.3016 0.9208 0.2251 -0.5435 0.4102 -0.5529 0.6158 -0.0711 0.0884 0.3214 0.0715 -0.24 0.1926 -1.6424 1.7515 0.0181 -0.0805 -0.5798 0.6071 0.2926 -0.2814 0.1362 -0.3261 -0.2071 -0.0769 0.3152 -0.243 0.0606 0.0165 0.0477 0.0361 -0.0385 0.1091 -0.0354 0.072 Enrichment: -8.4128 -17.876 15.3413 11.59 -35.532 51.8108 -19.5362 28.1401 10.2371 27.0233 -29.9791 -2.9721 7.8482 1.6571 10.2574 -13.878 -14.2023 -9.8501 16.502 -12.4251 20.5571 41.7022 -3.4687 42.1061 -19.2084 15.042 -22.3697 -8.1696 23.3761 8.5289 -17.0346 21.8269 -12.5537 10.7104 -16.5142 6.5921 13.6751 17.1517 -18.0626 8.6103 -46.9043 47.9297 21.7633 -26.7455 -124.6488 108.8359 8.3331 -5.0117 8.5056 -20.0588 -15.0086 -2.3613 10.7075 -3.8858 35.6667 5.266 26.6144 10.229 -51.5062 35.1584 -15.114 8.3135 Coefficients: -1.1095e-08 -2.3576e-08 2.0233e-08 1.5286e-08 -4.6862e-08 6.8331e-08 -2.5766e-08 3.7113e-08 1.3501e-08 3.5640e-08 -3.9538e-08 -3.9198e-09 1.0351e-08 2.1855e-09 1.3528e-08 -1.8303e-08 -1.8731e-08 -1.2991e-08 2.1764e-08 -1.6387e-08 2.7112e-08 5.4999e-08 -4.5747e-09 5.5532e-08 -2.5333e-08 1.9838e-08 -2.9502e-08 -1.0775e-08 3.0830e-08 1.1248e-08 -2.2466e-08 2.8787e-08 -1.6557e-08 1.4125e-08 -2.1780e-08 8.6940e-09 1.8035e-08 2.2621e-08 -2.3822e-08 1.1356e-08 -6.1860e-08 6.3212e-08 2.8703e-08 -3.5273e-08 -1.6439e-07 1.4354e-07 1.0990e-08 -6.6097e-09 1.1218e-08 -2.6455e-08 -1.9794e-08 -3.1143e-09 1.4122e-08 -5.1249e-09 4.7039e-08 6.9451e-09 3.5101e-08 1.3491e-08 -6.7929e-08 4.6369e-08 -1.9933e-08 1.0964e-08 Coefficient SE: 3.3509e-08 3.8386e-08 3.8432e-08 3.9911e-08 4.1018e-08 4.4619e-08 2.9732e-08 3.4877e-08 3.5090e-08 3.3119e-08 3.9821e-08 1.8303e-08 2.1767e-08 7.6020e-09 4.3948e-08 2.6039e-08 1.6870e-08 1.2412e-08 2.0824e-08 1.7220e-08 1.4446e-08 7.3710e-08 3.2292e-08 4.3949e-08 2.3392e-08 2.1388e-08 1.2962e-08 3.3356e-08 3.2255e-08 2.1219e-08 2.1950e-08 1.4283e-08 1.5880e-08 1.3359e-08 3.1727e-08 2.0848e-08 1.8765e-08 2.8186e-08 1.8108e-08 1.6559e-08 2.7558e-08 2.7699e-08 6.1518e-08 2.7134e-08 6.3448e-08 5.4732e-08 1.3394e-08 1.1091e-08 1.0931e-07 1.0885e-07 1.9422e-08 1.6229e-08 8.9583e-09 8.1858e-09 6.4892e-08 4.2363e-08 5.4675e-08 3.1346e-08 6.4174e-08 3.2789e-08 3.8061e-08 1.9726e-08 Lambda GC: 1.0895 Mean Chi^2: 1.1365 Intercept: 0.986 (0.0075) Ratio < 0 (usually indicates GC correction). Analysis finished at Sat Jun 22 17:13:40 2024 Total time elapsed: 2.0m:55.79s