********************************************************************* * 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/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.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 Mon Jun 24 01:54:50 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/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, 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 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: -0.0004 -0.0006 0.0009 0.0006 -0.0022 0.003 -0.0007 0.0009 0.0003 0.0011 0.0008 -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 0.0028 -0.0115 -0.0052 0.0159 0.0038 -0.0094 0.007 -0.0095 0.0106 -0.0012 0.0015 0.0055 0.0012 -0.0041 0.0033 -0.0285 0.0303 0.0003 -0.0014 -0.01 0.0104 0.005 -0.0048 0.0024 -0.0057 -0.0035 -0.0013 0.0054 -0.0042 0.0011 0.0003 0.0008 0.0006 -0.0007 0.0019 -0.0006 0.0012 Observed scale h2 SE: 0.0012 0.0009 0.0018 0.0015 0.0019 0.0019 0.0008 0.001 0.0009 0.0011 0.0032 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 0.0051 0.0161 0.0166 0.0073 0.0091 0.0036 0.0091 0.01 0.0018 0.0036 0.0057 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 0.0035 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: -0.0251 -0.0343 0.0493 0.0336 -0.129 0.1719 -0.0426 0.0505 0.0169 0.0616 0.0483 -0.0807 -0.0248 0.0326 0.0605 0.0241 -0.0882 -0.2145 -0.4992 0.2266 -0.2519 1.0097 0.0187 -0.0065 0.1852 -0.1641 0.1608 -0.6691 -0.3039 0.923 0.2215 -0.5426 0.4048 -0.5535 0.6169 -0.0701 0.0881 0.3194 0.0718 -0.2392 0.1916 -1.6523 1.7591 0.018 -0.079 -0.5779 0.6055 0.2911 -0.2813 0.1378 -0.3281 -0.2057 -0.0763 0.3157 -0.2433 0.0628 0.0158 0.0476 0.036 -0.0383 0.1094 -0.0357 0.0711 Enrichment: -10.2311 -19.1803 13.9563 11.7289 -37.255 50.517 -20.8272 26.1998 8.9456 25.6638 4.5085 -30.4213 -2.9344 7.9476 1.6626 10.9175 -14.1129 -14.3087 -9.9244 16.7426 -12.5603 20.7161 41.8277 -3.5482 42.3286 -19.3024 15.3799 -22.8053 -8.3211 23.6846 8.4821 -17.1913 21.7737 -12.7045 10.8441 -16.4527 6.644 13.7361 17.404 -18.1932 8.6572 -47.6951 48.6582 21.8831 -26.5404 -125.5866 109.714 8.3789 -5.0646 8.6997 -20.4021 -15.0691 -2.3704 10.8424 -3.9332 37.3726 5.0798 26.8226 10.2986 -51.8401 35.6386 -15.404 8.2892 Coefficients: -1.3366e-08 -2.5057e-08 1.8233e-08 1.5323e-08 -4.8671e-08 6.5996e-08 -2.7209e-08 3.4228e-08 1.1687e-08 3.3528e-08 5.8900e-09 -3.9743e-08 -3.8335e-09 1.0383e-08 2.1721e-09 1.4263e-08 -1.8437e-08 -1.8693e-08 -1.2965e-08 2.1873e-08 -1.6409e-08 2.7064e-08 5.4644e-08 -4.6354e-09 5.5299e-08 -2.5217e-08 2.0093e-08 -2.9793e-08 -1.0871e-08 3.0942e-08 1.1081e-08 -2.2459e-08 2.8446e-08 -1.6597e-08 1.4167e-08 -2.1494e-08 8.6799e-09 1.7945e-08 2.2737e-08 -2.3768e-08 1.1310e-08 -6.2310e-08 6.3568e-08 2.8589e-08 -3.4673e-08 -1.6407e-07 1.4333e-07 1.0946e-08 -6.6165e-09 1.1365e-08 -2.6654e-08 -1.9687e-08 -3.0968e-09 1.4165e-08 -5.1384e-09 4.8824e-08 6.6363e-09 3.5042e-08 1.3454e-08 -6.7725e-08 4.6559e-08 -2.0124e-08 1.0829e-08 Coefficient SE: 3.5818e-08 3.8501e-08 3.9345e-08 3.9942e-08 4.2375e-08 4.3124e-08 3.0347e-08 3.7826e-08 3.5626e-08 3.3265e-08 2.2622e-08 3.9791e-08 1.8265e-08 2.1764e-08 7.6016e-09 4.3472e-08 2.5930e-08 1.6861e-08 1.2387e-08 2.0830e-08 1.7223e-08 1.4405e-08 7.3657e-08 3.2306e-08 4.3844e-08 2.3398e-08 2.1494e-08 1.3173e-08 3.3336e-08 3.2220e-08 2.1172e-08 2.1944e-08 1.4532e-08 1.5850e-08 1.3360e-08 3.1791e-08 2.0829e-08 1.8726e-08 2.8193e-08 1.8089e-08 1.6544e-08 2.7557e-08 2.7712e-08 6.1484e-08 2.7017e-08 6.3553e-08 5.4789e-08 1.3365e-08 1.1087e-08 1.0930e-07 1.0883e-07 1.9421e-08 1.6231e-08 8.9695e-09 8.1906e-09 6.5208e-08 4.2694e-08 5.4675e-08 3.1341e-08 6.4189e-08 3.2867e-08 3.8111e-08 1.9789e-08 Lambda GC: 1.0895 Mean Chi^2: 1.1365 Intercept: 0.9859 (0.0076) Ratio < 0 (usually indicates GC correction). Analysis finished at Mon Jun 24 01:58:10 2024 Total time elapsed: 3.0m:20.29s