********************************************************************* * 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/DrnkWk_AFR-Saunders_2022.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.mergedReg2Map.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.DrinksPerWeek-Saunders_2022.AFR \ --w-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/weights/1000G.AFR.weights.hm3_noMHC. \ --print-coefficients Beginning analysis at Fri Jun 28 13:40:51 2024 Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/DrnkWk_AFR-Saunders_2022.sumstats.gz ... Read summary statistics for 1140612 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.mergedReg2Map.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, 1132830 SNPs remain. After merging with regression SNP LD, 1132830 SNPs remain. Removed 0 SNPs with chi^2 > 80 (1132830 SNPs remain) Total Observed scale h2: 0.1093 (0.0939) 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.mergedReg2Map_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 0.0119 -0.0544 0.0828 -0.0936 0.0569 -0.0527 0.0282 -0.0121 -0.0739 0.1113 0.0031 -0.1065 -0.0711 -0.0629 0.0753 -0.1514 -0.0809 0.037 0.2209 -0.0021 -0.0711 0.001 -0.0044 -0.0066 0.0306 -0.0366 -0.4694 0.0098 0.2064 0.1089 -0.5133 0.1325 0.4378 0.2117 -0.0597 -0.0051 0.1431 0.0367 -0.0673 0.1709 0.4689 -0.4228 -0.0305 0.035 0.1812 -0.1707 0.1483 0.0404 0.3784 -0.441 -0.0159 -0.2609 -0.0101 0.0227 -0.0031 0.0278 0.0544 -0.0443 0.0416 -0.035 0.0228 -0.0281 Observed scale h2 SE: 0.0461 0.0322 0.0797 0.0615 0.0806 0.0645 0.0426 0.0282 0.0325 0.0347 0.1254 0.0554 0.076 0.0448 0.1568 0.0424 0.0675 0.1161 0.2986 0.1548 0.2215 0.363 0.0182 0.0324 0.075 0.1108 0.1334 0.1967 0.5246 0.5509 0.2893 0.3205 0.1416 0.3346 0.4244 0.0646 0.1463 0.1704 0.0677 0.1391 0.1803 0.4137 0.4286 0.0243 0.0425 0.1221 0.1234 0.2338 0.291 0.7343 0.7379 0.1159 0.2038 0.1674 0.3129 0.0437 0.0686 0.0453 0.054 0.0211 0.041 0.0417 0.0782 Proportion of SNPs: 0.0024 0.0016 0.0042 0.0032 0.0041 0.0031 0.0029 0.0019 0.0019 0.0024 0.0123 0.0026 0.0084 0.0039 0.0361 0.0022 0.0063 0.0149 0.0502 0.0134 0.02 0.0486 0.0004 0.0018 0.0043 0.0085 0.0104 0.0292 0.0364 0.0389 0.026 0.0314 0.0185 0.0434 0.0567 0.0042 0.0132 0.0231 0.0041 0.013 0.022 0.0345 0.036 0.0008 0.003 0.0046 0.0055 0.0348 0.0557 0.0158 0.016 0.0136 0.0321 0.029 0.0618 0.0017 0.0031 0.0018 0.0035 0.0007 0.003 0.0023 0.0085 Proportion of h2g: 0.2571 0.1091 -0.4978 0.7582 -0.8565 0.5212 -0.4821 0.2577 -0.1104 -0.6768 1.0183 0.0285 -0.975 -0.6509 -0.5753 0.6892 -1.3855 -0.7403 0.3388 2.0216 -0.0196 -0.6511 0.0091 -0.04 -0.0605 0.2804 -0.3353 -4.296 0.0897 1.889 0.9971 -4.6979 1.213 4.0074 1.9374 -0.5461 -0.0462 1.3102 0.3358 -0.6161 1.5641 4.2915 -3.8694 -0.2789 0.3202 1.6586 -1.5619 1.3574 0.3693 3.4637 -4.0359 -0.1455 -2.3883 -0.0922 0.2081 -0.028 0.2541 0.4977 -0.4053 0.3806 -0.3202 0.2084 -0.2575 Enrichment: 105.6865 67.5935 -117.5501 235.2133 -210.272 169.969 -168.0946 134.9674 -58.8914 -284.3317 82.7414 10.9893 -116.5034 -165.1478 -15.9282 311.5731 -221.5032 -49.6309 6.7493 150.3221 -0.9835 -13.3919 20.7501 -22.1359 -13.9295 33.1599 -32.3331 -146.9912 2.4613 48.5823 38.3449 -149.4086 65.5927 92.2846 34.1503 -128.9772 -3.5062 56.6143 82.337 -47.2253 71.0949 124.3356 -107.5345 -341.3234 108.2294 362.4005 -284.6153 39.0243 6.636 219.6526 -252.0921 -10.721 -74.3548 -3.1778 3.3686 -16.7718 82.4551 282.6798 -116.4627 528.5765 -105.3755 90.6616 -30.1553 Coefficients: 9.1198e-07 5.8327e-07 -1.0144e-06 2.0297e-06 -1.8145e-06 1.4667e-06 -1.4505e-06 1.1647e-06 -5.0818e-07 -2.4535e-06 7.1399e-07 9.4828e-08 -1.0053e-06 -1.4251e-06 -1.3745e-07 2.6886e-06 -1.9114e-06 -4.2827e-07 5.8241e-08 1.2971e-06 -8.4870e-09 -1.1556e-07 1.7906e-07 -1.9101e-07 -1.2020e-07 2.8614e-07 -2.7901e-07 -1.2684e-06 2.1239e-08 4.1922e-07 3.3088e-07 -1.2893e-06 5.6601e-07 7.9634e-07 2.9469e-07 -1.1130e-06 -3.0255e-08 4.8853e-07 7.1050e-07 -4.0751e-07 6.1349e-07 1.0729e-06 -9.2793e-07 -2.9453e-06 9.3393e-07 3.1272e-06 -2.4560e-06 3.3675e-07 5.7263e-08 1.8954e-06 -2.1753e-06 -9.2513e-08 -6.4162e-07 -2.7422e-08 2.9068e-08 -1.4473e-07 7.1152e-07 2.4393e-06 -1.0050e-06 4.5612e-06 -9.0930e-07 7.8233e-07 -2.6021e-07 Coefficient SE: 1.4956e-06 1.5765e-06 1.4862e-06 1.5075e-06 1.5637e-06 1.6618e-06 1.1723e-06 1.1677e-06 1.3681e-06 1.1509e-06 8.0452e-07 1.6843e-06 7.1684e-07 8.9677e-07 3.4283e-07 1.5153e-06 8.5184e-07 6.1450e-07 4.6979e-07 9.0888e-07 8.7667e-07 5.8970e-07 3.2680e-06 1.4178e-06 1.3638e-06 1.0347e-06 1.0156e-06 5.3164e-07 1.1372e-06 1.1191e-06 8.7863e-07 8.0509e-07 6.0494e-07 6.0851e-07 5.9087e-07 1.2050e-06 8.7641e-07 5.8165e-07 1.3113e-06 8.4214e-07 6.4725e-07 9.4656e-07 9.4081e-07 2.3499e-06 1.1337e-06 2.1072e-06 1.7759e-06 5.3086e-07 4.1300e-07 3.6775e-06 3.6403e-06 6.7441e-07 5.0103e-07 4.5553e-07 3.9994e-07 2.0686e-06 1.7591e-06 2.0337e-06 1.2259e-06 2.3147e-06 1.0665e-06 1.4331e-06 7.2304e-07 Lambda GC: 1.0375 Mean Chi^2: 1.0355 Intercept: 1.0265 (0.0058) Ratio: 0.7469 (0.1641) Analysis finished at Fri Jun 28 13:56:55 2024 Total time elapsed: 16.0m:3.49s