********************************************************************* * 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/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 Sat Jun 22 17:10:45 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/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: 5527.2168 (469.4311) 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: 170.0616 -97.4612 176.9089 291.8591 -302.1756 -389.3366 -41.9646 -132.3142 -174.2903 422.0794 -321.0522 -660.5446 1198.0632 1276.578 601.5529 -1494.1916 720.5563 600.8913 736.8345 1659.1267 -62.5838 42.4322 -91.3024 117.1226 -123.0469 -8.0438 -1948.6915 -5730.2302 6118.9473 42.1452 341.1802 -544.0597 1509.2562 -699.9641 -187.6755 494.8759 931.0025 131.2693 2059.6451 -405.6779 4432.8164 -4290.3456 249.8518 -447.1397 -207.4138 403.6153 442.2408 -1910.7111 1127.6623 -539.1681 -57.1265 159.1503 -932.5953 1510.0935 20.5815 -454.6199 534.0201 -558.4761 110.9675 -129.7044 446.8316 -611.0953 Observed scale h2 SE: 266.9722 227.7597 456.035 429.5968 457.4035 418.6976 230.3636 177.9742 249.6542 366.1101 294.0438 450.2597 284.0133 822.7605 237.7755 403.7009 838.9606 1684.7835 1028.8178 1424.6801 2153.1403 122.9056 214.4711 475.9049 651.0213 879.2696 1158.7049 3038.4244 3247.8496 1490.8702 1622.0657 886.0436 1939.9366 2233.2136 376.242 824.6912 1126.8757 440.7503 912.3402 1089.2328 2220.8527 2315.3461 158.4517 257.1702 746.8287 771.8791 1562.4633 1713.0185 4398.1294 4360.6188 782.924 1275.039 1110.3 1715.2655 292.8244 384.6197 291.4925 351.2325 132.5318 264.1604 287.7859 488.3412 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: 0.0308 -0.0176 0.032 0.0528 -0.0547 -0.0704 -0.0076 -0.0239 -0.0315 0.0764 -0.0581 -0.1195 0.2168 0.231 0.1088 -0.2703 0.1304 0.1087 0.1333 0.3002 -0.0113 0.0077 -0.0165 0.0212 -0.0223 -0.0015 -0.3526 -1.0367 1.1071 0.0076 0.0617 -0.0984 0.2731 -0.1266 -0.034 0.0895 0.1684 0.0237 0.3726 -0.0734 0.802 -0.7762 0.0452 -0.0809 -0.0375 0.073 0.08 -0.3457 0.204 -0.0975 -0.0103 0.0288 -0.1687 0.2732 0.0037 -0.0823 0.0966 -0.101 0.0201 -0.0235 0.0808 -0.1106 Enrichment: 12.4152 -9.7615 8.9554 18.2404 -15.6245 -20.4793 -3.6704 -12.2894 -16.5356 31.4495 -21.6501 -13.9908 52.2221 6.2809 48.7015 -42.787 8.6016 2.1382 9.7445 14.8089 -0.2298 17.0293 -8.9551 4.7901 -2.5908 -0.1377 -11.8886 -28.0826 28.1037 0.2889 1.9347 -5.2378 6.2003 -2.2024 -7.8864 6.6763 7.1664 5.699 28.0407 -3.2805 22.9031 -21.2411 54.4999 -26.8861 -8.0672 13.0905 2.2787 -6.1568 12.7379 -6.0001 -0.749 0.8845 -5.7322 4.3691 2.1917 -26.2412 53.8911 -28.5982 26.8715 -7.5614 34.481 -12.7589 Coefficients: 5.2584e-03 -4.1344e-03 3.7930e-03 7.7256e-03 -6.6177e-03 -8.6739e-03 -1.5546e-03 -5.2051e-03 -7.0036e-03 1.3320e-02 -9.1698e-03 -5.9257e-03 2.2118e-02 2.6602e-03 2.0627e-02 -1.8122e-02 3.6431e-03 9.0564e-04 4.1272e-03 6.2722e-03 -9.7338e-05 7.2127e-03 -3.7929e-03 2.0288e-03 -1.0973e-03 -5.8315e-05 -5.0354e-03 -1.1894e-02 1.1903e-02 1.2235e-04 8.1941e-04 -2.2185e-03 2.6261e-03 -9.3283e-04 -3.3403e-03 2.8277e-03 3.0353e-03 2.4138e-03 1.1876e-02 -1.3894e-03 9.7005e-03 -8.9965e-03 2.3083e-02 -1.1387e-02 -3.4168e-03 5.5444e-03 9.6513e-04 -2.6077e-03 5.3950e-03 -2.5413e-03 -3.1724e-04 3.7461e-04 -2.4278e-03 1.8505e-03 9.2826e-04 -1.1114e-02 2.2825e-02 -1.2113e-02 1.1381e-02 -3.2026e-03 1.4604e-02 -5.4040e-03 Coefficient SE: 0.0083 0.0097 0.0098 0.0114 0.01 0.0093 0.0085 0.007 0.01 0.0116 0.0084 0.004 0.0052 0.0017 0.0082 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 0.0206 0.0043 0.003 0.0029 0.0021 0.0132 0.0094 0.0125 0.0076 0.0136 0.0065 0.0094 0.0043 Lambda GC: 1.1491 Mean Chi^2: 1.2158 Intercept: 1.0144 (0.0101) Ratio: 0.0668 (0.0469) Analysis finished at Sat Jun 22 17:13:41 2024 Total time elapsed: 2.0m:56.91s