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LD Score Regression (LDSC)
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heritability obtain using --h2 and --rg are different. #207

Open fhormoz opened 4 years ago

fhormoz commented 4 years ago

I am using ldsc to compute the genetic correlation between two traits. However, the heritability estimates in the process of computing is different from heritability computed using --h2. have computed the genetic correlation of IOP and VCDR and you can see from the log the hg2 is estimated to be -2.3276 (8.4352) when --rg option is used. However, the heritability of IOP is estimated to be 0.12 (0.0297). This difference make be concern regarding the genetic correlation estimates. In some cases, this difference cause the genetic correlation to be nan out of bound as h2 for one of traits was estimated really high and out of bound. Why the --rg heritability is not the same as --h2?

One possible solution is to use --no-intercept when computing the --rg as you can see the intercept for IOP in --rg is not 1. This may solve the problem here but in other datasets this can cause a reverse problem.

Here is the log of genetic correlation: ~/Software/S_LDSC/ldsc/ldsc.py --rg Meta_IOP_age_sex_caucasians_MAF0.01_20160806.sumstats.gz,vcdr_visit_int.sumstats.gz --ref-ld-chr annot_uk10k/baselineLD. --w-ld-chr annot_uk10k/weight.

Beginning analysis at Wed May 13 09:19:49 2020 Reading summary statistics from Meta_IOP_age_sex_caucasians_MAF0.01_20160806.sumstats.gz ... Read summary statistics for 1200645 SNPs. Reading reference panel LD Score from annot_uk10k/baselineLD.[1-22] ... Read reference panel LD Scores for 8743917 SNPs. Removing partitioned LD Scores with zero variance. Reading regression weight LD Score from annot_uk10k/weight.[1-22] ... Read regression weight LD Scores for 8743917 SNPs. After merging with reference panel LD, 1164815 SNPs remain. After merging with regression SNP LD, 1164815 SNPs remain. Computing rg for phenotype 2/2 Reading summary statistics from vcdr_visit_int.sumstats.gz ... Read summary statistics for 1217311 SNPs. After merging with summary statistics, 1164815 SNPs remain. 1137518 SNPs with valid alleles. /usr/local/google/home/fhormoz/Software/S_LDSC/ldsc/ldscore/irwls.py:161: FutureWarning: rcond parameter will change to the default of machine precision times max(M, N) where M and N are the input matrix dimensions. To use the future default and silence this warning we advise to pass rcond=None, to keep using the old, explicitly pass rcond=-1. coef = np.linalg.lstsq(x, y)

Heritability of phenotype 1

Total Observed scale h2: -2.3276 (8.4352) Categories: baseL2_0 Coding_UCSCL2_0 Coding_UCSC.extend.500L2_0 Conserved_LindbladTohL2_0 Conserved_LindbladToh.extend.500L2_0 CTCF_HoffmanL2_0 CTCF_Hoffman.extend.500L2_0 DGF_ENCODEL2_0 DGF_ENCODE.extend.500L2_0 DHS_peaks_TrynkaL2_0 DHS_TrynkaL2_0 DHS_Trynka.extend.500L2_0 Enhancer_AnderssonL2_0 Enhancer_Andersson.extend.500L2_0 Enhancer_HoffmanL2_0 Enhancer_Hoffman.extend.500L2_0 FetalDHS_TrynkaL2_0 FetalDHS_Trynka.extend.500L2_0 H3K27ac_HniszL2_0 H3K27ac_Hnisz.extend.500L2_0 H3K27ac_PGC2L2_0 H3K27ac_PGC2.extend.500L2_0 H3K4me1_peaks_TrynkaL2_0 H3K4me1_TrynkaL2_0 H3K4me1_Trynka.extend.500L2_0 H3K4me3_peaks_TrynkaL2_0 H3K4me3_TrynkaL2_0 H3K4me3_Trynka.extend.500L2_0 H3K9ac_peaks_TrynkaL2_0 H3K9ac_TrynkaL2_0 H3K9ac_Trynka.extend.500L2_0 Intron_UCSCL2_0 Intron_UCSC.extend.500L2_0 PromoterFlanking_HoffmanL2_0 PromoterFlanking_Hoffman.extend.500L2_0 Promoter_UCSCL2_0 Promoter_UCSC.extend.500L2_0 Repressed_HoffmanL2_0 Repressed_Hoffman.extend.500L2_0 SuperEnhancer_HniszL2_0 SuperEnhancer_Hnisz.extend.500L2_0 TFBS_ENCODEL2_0 TFBS_ENCODE.extend.500L2_0 Transcr_HoffmanL2_0 Transcr_Hoffman.extend.500L2_0 TSS_HoffmanL2_0 TSS_Hoffman.extend.500L2_0 UTR_3_UCSCL2_0 UTR_3_UCSC.extend.500L2_0 UTR_5_UCSCL2_0 UTR_5_UCSC.extend.500L2_0 WeakEnhancer_HoffmanL2_0 WeakEnhancer_Hoffman.extend.500L2_0 Super_Enhancer_VahediL2_0 Super_Enhancer_Vahedi.extend.500L2_0 Typical_Enhancer_VahediL2_0 Typical_Enhancer_Vahedi.extend.500L2_0 GERP.NSL2_0 GERP.RSsup4L2_0 MAFbin1L2_0 MAFbin2L2_0 MAFbin3L2_0 MAFbin4L2_0 MAFbin5L2_0 MAFbin6L2_0 MAFbin7L2_0 MAFbin8L2_0 MAFbin9L2_0 MAFbin10L2_0 MAF_Adj_Predicted_Allele_AgeL2_0 MAF_Adj_LLD_AFRL2_0 Recomb_Rate_10kbL2_0 Nucleotide_Diversity_10kbL2_0 Backgrd_Selection_StatL2_0 CpG_Content_50kbL2_0 Observed scale h2: 4.8973e+01 2.6934e+00 4.7256e-01 4.7304e-01 -1.5429e+01 -1.9738e+00 5.5524e-01 -2.3159e+00 -2.1750e+01 -2.3371e+01 4.7781e+01 -1.9130e+00 -2.0774e+00 1.1325e+00 -3.3810e+00 -3.8633e+00 -8.7008e+00 1.7186e+01 4.6574e+00 2.3096e+00 -4.2914e+01 3.3197e+01 9.2540e+00 1.8851e+01 -2.1217e+01 2.8599e+00 -1.0290e+01 3.2786e+00 5.9456e+00 8.6150e+00 -1.7177e+01 2.8023e+01 -2.7848e+01 4.5848e+00 -4.5265e-01 9.6133e-01 -3.2452e+00 -1.7094e+01 -1.4844e+01 5.3125e+01 -4.8509e+01 4.9467e+00 1.2290e+01 -1.2455e+01 1.5104e+01 -3.0575e-01 -2.4277e+00 1.0500e+00 -4.8463e+00 -1.3659e+00 6.4614e+00 1.5640e+00 -1.0654e+01 1.0943e+01 -1.1353e+01 2.4232e+00 -3.3257e+00 9.4362e+00 6.1415e-01 -1.2125e+00 -2.0123e+00 -6.0388e-01 -1.0307e+00 3.5122e+00 3.9811e-01 -6.0453e+00 2.8323e+00 -2.2483e+00 -3.2323e+00 1.3457e-01 3.1879e-02 -8.3446e-01 -1.0264e+01 -2.7669e+00 -3.6453e+00 Observed scale h2 SE: 60.2105 3.7976 7.4848 3.1132 17.9796 2.4258 5.398 14.445 32.2077 17.1399 24.3493 37.521 2.5366 4.2793 4.684 6.7043 9.7978 18.7924 58.8234 65.1299 39.8864 39.0946 15.4819 29.3097 34.7141 6.7479 14.8759 15.1577 7.7001 13.411 18.6934 83.6156 85.5729 2.7542 6.2359 5.8314 4.3647 24.6431 32.7234 99.1832 100.4388 15.0119 26.7919 19.4638 29.7342 4.4704 5.9218 2.9287 6.1551 1.2537 5.5076 4.7443 8.3176 23.4278 23.5219 7.8163 8.6535 19.8704 1.7502 4.2189 6.4 5.2595 6.5414 6.9589 5.9526 6.2459 7.484 4.0317 5.0624 0.3471 0.2661 4.7646 25.517 9.9817 18.3811 Proportion of SNPs: 4.8445e-02 7.1555e-04 3.1543e-03 1.3475e-03 1.6763e-02 1.1579e-03 3.4177e-03 6.9508e-03 2.6809e-02 5.7543e-03 8.6261e-03 2.5012e-02 2.1684e-04 9.4744e-04 2.1176e-03 4.4350e-03 4.3512e-03 1.4325e-02 1.9242e-02 2.0762e-02 1.3264e-02 1.6483e-02 8.7624e-03 2.1535e-02 3.0211e-02 2.0758e-03 6.6003e-03 1.2508e-02 1.9456e-03 6.2853e-03 1.1312e-02 1.8979e-02 1.9436e-02 4.1075e-04 1.5985e-03 1.4750e-03 1.8286e-03 2.2184e-02 3.4809e-02 8.2390e-03 8.3900e-03 6.6140e-03 1.7040e-02 1.6836e-02 3.7150e-02 8.6840e-04 1.6482e-03 5.5728e-04 1.2911e-03 2.6668e-04 1.2925e-03 1.0712e-03 4.3910e-03 1.0122e-03 1.0346e-03 1.0565e-03 1.2630e-03 9.0916e-02 4.3266e-04 3.8185e-03 4.8611e-03 4.8880e-03 4.9477e-03 4.8065e-03 4.8646e-03 4.8560e-03 4.8563e-03 4.8869e-03 4.7449e-03 7.4195e-04 -5.1573e-04 7.6007e-02 2.1951e-01 8.6205e-03 4.8217e-04 Proportion of h2g: -2.1040e+01 -1.1571e+00 -2.0302e-01 -2.0323e-01 6.6287e+00 8.4797e-01 -2.3854e-01 9.9495e-01 9.3441e+00 1.0041e+01 -2.0528e+01 8.2188e-01 8.9250e-01 -4.8656e-01 1.4525e+00 1.6598e+00 3.7380e+00 -7.3833e+00 -2.0009e+00 -9.9223e-01 1.8437e+01 -1.4262e+01 -3.9757e+00 -8.0988e+00 9.1151e+00 -1.2286e+00 4.4207e+00 -1.4085e+00 -2.5543e+00 -3.7012e+00 7.3795e+00 -1.2039e+01 1.1964e+01 -1.9697e+00 1.9447e-01 -4.1301e-01 1.3942e+00 7.3438e+00 6.3773e+00 -2.2823e+01 2.0840e+01 -2.1252e+00 -5.2800e+00 5.3508e+00 -6.4888e+00 1.3136e-01 1.0430e+00 -4.5108e-01 2.0821e+00 5.8682e-01 -2.7759e+00 -6.7191e-01 4.5772e+00 -4.7012e+00 4.8777e+00 -1.0410e+00 1.4288e+00 -4.0540e+00 -2.6385e-01 5.2091e-01 8.6450e-01 2.5944e-01 4.4282e-01 -1.5089e+00 -1.7103e-01 2.5972e+00 -1.2168e+00 9.6593e-01 1.3887e+00 -5.7814e-02 -1.3696e-02 3.5850e-01 4.4097e+00 1.1887e+00 1.5661e+00 Enrichment: -4.3430e+02 -1.6171e+03 -6.4362e+01 -1.5082e+02 3.9544e+02 7.3234e+02 -6.9797e+01 1.4314e+02 3.4854e+02 1.7449e+03 -2.3797e+03 3.2860e+01 4.1159e+03 -5.1355e+02 6.8593e+02 3.7424e+02 8.5908e+02 -5.1540e+02 -1.0399e+02 -4.7790e+01 1.3900e+03 -8.6525e+02 -4.5373e+02 -3.7608e+02 3.0172e+02 -5.9190e+02 6.6978e+02 -1.1261e+02 -1.3129e+03 -5.8886e+02 6.5234e+02 -6.3433e+02 6.1556e+02 -4.7954e+03 1.2166e+02 -2.8000e+02 7.6245e+02 3.3103e+02 1.8321e+02 -2.7702e+03 2.4839e+03 -3.2132e+02 -3.0986e+02 3.1783e+02 -1.7467e+02 1.5126e+02 6.3279e+02 -8.0944e+02 1.6126e+03 2.2004e+03 -2.1477e+03 -6.2723e+02 1.0424e+03 -4.6444e+03 4.7147e+03 -9.8536e+02 1.1312e+03 -4.4590e+01 -6.0984e+02 1.3642e+02 1.7784e+02 5.3076e+01 8.9500e+01 -3.1393e+02 -3.5159e+01 5.3483e+02 -2.5057e+02 1.9766e+02 2.9267e+02 -7.7922e+01 2.6556e+01 4.7166e+00 2.0089e+01 1.3789e+02 3.2480e+03 Coefficients: 9.3326e-06 3.4750e-05 1.3831e-06 3.2409e-06 -8.4975e-06 -1.5737e-05 1.4998e-06 -3.0759e-06 -7.4898e-06 -3.7496e-05 5.1137e-05 -7.0612e-07 -8.8446e-05 1.1036e-05 -1.4740e-05 -8.0419e-06 -1.8461e-05 1.1075e-05 2.2345e-06 1.0269e-06 -2.9868e-05 1.8593e-05 9.7500e-06 8.0815e-06 -6.4835e-06 1.2719e-05 -1.4393e-05 2.4198e-06 2.8213e-05 1.2654e-05 -1.4018e-05 1.3631e-05 -1.3228e-05 1.0305e-04 -2.6143e-06 6.0168e-06 -1.6384e-05 -7.1135e-06 -3.9369e-06 5.9527e-05 -5.3377e-05 6.9047e-06 6.6584e-06 -6.8297e-06 3.7533e-06 -3.2504e-06 -1.3598e-05 1.7394e-05 -3.4652e-05 -4.7284e-05 4.6152e-05 1.3478e-05 -2.2400e-05 9.9802e-05 -1.0131e-04 2.1174e-05 -2.4309e-05 9.5819e-07 1.3105e-05 -2.9314e-06 -3.8216e-06 -1.1405e-06 -1.9233e-06 6.7460e-06 7.5552e-07 -1.1493e-05 5.3844e-06 -4.2474e-06 -6.2890e-06 1.6745e-06 -5.7066e-07 -1.0135e-07 -4.3169e-07 -2.9632e-06 -6.9795e-05 Coefficient SE: 1.1474e-05 4.8996e-05 2.1906e-05 2.1329e-05 9.9021e-06 1.9341e-05 1.4581e-05 1.9186e-05 1.1091e-05 2.7499e-05 2.6060e-05 1.3849e-05 1.0799e-04 4.1698e-05 2.0420e-05 1.3956e-05 2.0788e-05 1.2111e-05 2.8222e-05 2.8960e-05 2.7761e-05 2.1897e-05 1.6312e-05 1.2565e-05 1.0608e-05 3.0011e-05 2.0807e-05 1.1187e-05 3.6538e-05 1.9698e-05 1.5256e-05 4.0673e-05 4.0647e-05 6.1903e-05 3.6015e-05 3.6498e-05 2.2036e-05 1.0255e-05 8.6788e-06 1.1114e-04 1.1052e-04 2.0954e-05 1.4515e-05 1.0673e-05 7.3891e-06 4.7525e-05 3.3169e-05 4.8518e-05 4.4011e-05 4.3399e-05 3.9339e-05 4.0887e-05 1.7488e-05 2.1367e-04 2.0990e-04 6.8301e-05 6.3252e-05 2.0177e-06 3.7346e-05 1.0200e-05 1.2155e-05 9.9335e-06 1.2206e-05 1.3366e-05 1.1297e-05 1.1874e-05 1.4227e-05 7.6164e-06 9.8496e-06 4.3188e-06 4.7640e-06 5.7872e-07 1.0732e-06 1.0690e-05 3.5194e-04 Lambda GC: 1.0802 Mean Chi^2: 1.0944 Intercept: 0.7197 (0.4393) Ratio < 0 (usually indicates GC correction).

Heritability of phenotype 2/2

Total Observed scale h2: 0.5032 (0.0624) Categories: baseL2_0 Coding_UCSCL2_0 Coding_UCSC.extend.500L2_0 Conserved_LindbladTohL2_0 Conserved_LindbladToh.extend.500L2_0 CTCF_HoffmanL2_0 CTCF_Hoffman.extend.500L2_0 DGF_ENCODEL2_0 DGF_ENCODE.extend.500L2_0 DHS_peaks_TrynkaL2_0 DHS_TrynkaL2_0 DHS_Trynka.extend.500L2_0 Enhancer_AnderssonL2_0 Enhancer_Andersson.extend.500L2_0 Enhancer_HoffmanL2_0 Enhancer_Hoffman.extend.500L2_0 FetalDHS_TrynkaL2_0 FetalDHS_Trynka.extend.500L2_0 H3K27ac_HniszL2_0 H3K27ac_Hnisz.extend.500L2_0 H3K27ac_PGC2L2_0 H3K27ac_PGC2.extend.500L2_0 H3K4me1_peaks_TrynkaL2_0 H3K4me1_TrynkaL2_0 H3K4me1_Trynka.extend.500L2_0 H3K4me3_peaks_TrynkaL2_0 H3K4me3_TrynkaL2_0 H3K4me3_Trynka.extend.500L2_0 H3K9ac_peaks_TrynkaL2_0 H3K9ac_TrynkaL2_0 H3K9ac_Trynka.extend.500L2_0 Intron_UCSCL2_0 Intron_UCSC.extend.500L2_0 PromoterFlanking_HoffmanL2_0 PromoterFlanking_Hoffman.extend.500L2_0 Promoter_UCSCL2_0 Promoter_UCSC.extend.500L2_0 Repressed_HoffmanL2_0 Repressed_Hoffman.extend.500L2_0 SuperEnhancer_HniszL2_0 SuperEnhancer_Hnisz.extend.500L2_0 TFBS_ENCODEL2_0 TFBS_ENCODE.extend.500L2_0 Transcr_HoffmanL2_0 Transcr_Hoffman.extend.500L2_0 TSS_HoffmanL2_0 TSS_Hoffman.extend.500L2_0 UTR_3_UCSCL2_0 UTR_3_UCSC.extend.500L2_0 UTR_5_UCSCL2_0 UTR_5_UCSC.extend.500L2_0 WeakEnhancer_HoffmanL2_0 WeakEnhancer_Hoffman.extend.500L2_0 Super_Enhancer_VahediL2_0 Super_Enhancer_Vahedi.extend.500L2_0 Typical_Enhancer_VahediL2_0 Typical_Enhancer_Vahedi.extend.500L2_0 GERP.NSL2_0 GERP.RSsup4L2_0 MAFbin1L2_0 MAFbin2L2_0 MAFbin3L2_0 MAFbin4L2_0 MAFbin5L2_0 MAFbin6L2_0 MAFbin7L2_0 MAFbin8L2_0 MAFbin9L2_0 MAFbin10L2_0 MAF_Adj_Predicted_Allele_AgeL2_0 MAF_Adj_LLD_AFRL2_0 Recomb_Rate_10kbL2_0 Nucleotide_Diversity_10kbL2_0 Backgrd_Selection_StatL2_0 CpG_Content_50kbL2_0 Observed scale h2: -2.6989e-01 1.1199e-02 -5.4743e-02 1.3574e-01 2.3919e-02 -1.0517e-01 1.4031e-02 -6.2331e-02 -1.1081e-02 1.0623e-01 3.8772e-01 1.0559e-01 3.0452e-03 -2.3498e-02 1.8273e-01 -1.9890e-01 4.2803e-02 -1.0393e-01 5.4457e-01 -6.2790e-01 2.0003e-01 -1.5238e-01 -8.3230e-02 -3.3794e-02 2.1154e-01 -8.5423e-02 2.5764e-01 -2.1547e-01 8.8575e-02 -1.2615e-01 4.3727e-01 1.2126e+00 -1.3097e+00 -6.8547e-02 1.2758e-02 -3.5391e-02 2.0584e-02 -3.3289e-01 1.8801e-01 1.2726e-01 -1.4626e-01 4.5419e-02 -1.8726e-01 -2.0729e-01 3.7562e-01 1.3676e-02 5.7125e-03 -3.8580e-02 8.1841e-02 -1.7902e-02 3.3294e-02 -3.8928e-02 -2.2580e-02 4.9789e-02 -6.0560e-02 1.3024e-01 -1.3967e-01 -1.6183e-01 3.6095e-02 1.7752e-02 3.2722e-02 2.9414e-02 3.8788e-02 3.0830e-02 7.2434e-02 3.7388e-02 4.9308e-02 7.9806e-02 9.3225e-02 -1.2261e-03 8.2798e-04 -3.8272e-02 -7.9436e-02 4.8198e-02 -7.2834e-02 Observed scale h2 SE: 6.1728e-01 3.4906e-02 5.5432e-02 8.4783e-02 1.5192e-01 1.0227e-01 1.2625e-01 1.3234e-01 2.1230e-01 2.0777e-01 4.1256e-01 3.5433e-01 1.9502e-02 3.0064e-02 8.2483e-02 1.2070e-01 1.2469e-01 2.6382e-01 4.5267e-01 4.8597e-01 3.4622e-01 4.0671e-01 1.2000e-01 2.3617e-01 2.4984e-01 7.7297e-02 1.4405e-01 1.7430e-01 1.0706e-01 1.2847e-01 1.7255e-01 9.6479e-01 9.6913e-01 3.6625e-02 5.6747e-02 1.3098e-01 1.3077e-01 3.5696e-01 4.1183e-01 8.0760e-01 8.1708e-01 9.7129e-02 2.0866e-01 2.7606e-01 2.9806e-01 4.0379e-02 6.2382e-02 4.4926e-02 9.2838e-02 2.1389e-02 4.2444e-02 3.7342e-02 8.7412e-02 1.5206e-01 1.5609e-01 1.1334e-01 1.0952e-01 2.5850e-01 3.7414e-02 9.7230e-03 1.5938e-02 1.0082e-02 2.3224e-02 2.0678e-02 2.4528e-02 1.4742e-02 2.3682e-02 3.4045e-02 2.6098e-02 1.8287e-03 9.5291e-04 3.9545e-02 1.0478e-01 3.3114e-02 1.0362e-01 Proportion of SNPs: 4.8445e-02 7.1555e-04 3.1543e-03 1.3475e-03 1.6763e-02 1.1579e-03 3.4177e-03 6.9508e-03 2.6809e-02 5.7543e-03 8.6261e-03 2.5012e-02 2.1684e-04 9.4744e-04 2.1176e-03 4.4350e-03 4.3512e-03 1.4325e-02 1.9242e-02 2.0762e-02 1.3264e-02 1.6483e-02 8.7624e-03 2.1535e-02 3.0211e-02 2.0758e-03 6.6003e-03 1.2508e-02 1.9456e-03 6.2853e-03 1.1312e-02 1.8979e-02 1.9436e-02 4.1075e-04 1.5985e-03 1.4750e-03 1.8286e-03 2.2184e-02 3.4809e-02 8.2390e-03 8.3900e-03 6.6140e-03 1.7040e-02 1.6836e-02 3.7150e-02 8.6840e-04 1.6482e-03 5.5728e-04 1.2911e-03 2.6668e-04 1.2925e-03 1.0712e-03 4.3910e-03 1.0122e-03 1.0346e-03 1.0565e-03 1.2630e-03 9.0916e-02 4.3266e-04 3.8185e-03 4.8611e-03 4.8880e-03 4.9477e-03 4.8065e-03 4.8646e-03 4.8560e-03 4.8563e-03 4.8869e-03 4.7449e-03 7.4195e-04 -5.1573e-04 7.6007e-02 2.1951e-01 8.6205e-03 4.8217e-04 Proportion of h2g: -5.3636e-01 2.2256e-02 -1.0879e-01 2.6976e-01 4.7535e-02 -2.0900e-01 2.7884e-02 -1.2387e-01 -2.2022e-02 2.1111e-01 7.7053e-01 2.0984e-01 6.0519e-03 -4.6698e-02 3.6315e-01 -3.9528e-01 8.5064e-02 -2.0655e-01 1.0822e+00 -1.2478e+00 3.9753e-01 -3.0284e-01 -1.6541e-01 -6.7159e-02 4.2041e-01 -1.6977e-01 5.1201e-01 -4.2822e-01 1.7603e-01 -2.5070e-01 8.6900e-01 2.4099e+00 -2.6029e+00 -1.3623e-01 2.5354e-02 -7.0334e-02 4.0907e-02 -6.6156e-01 3.7365e-01 2.5291e-01 -2.9066e-01 9.0263e-02 -3.7215e-01 -4.1196e-01 7.4648e-01 2.7179e-02 1.1353e-02 -7.6671e-02 1.6265e-01 -3.5577e-02 6.6165e-02 -7.7363e-02 -4.4873e-02 9.8948e-02 -1.2035e-01 2.5883e-01 -2.7758e-01 -3.2162e-01 7.1734e-02 3.5279e-02 6.5030e-02 5.8455e-02 7.7084e-02 6.1269e-02 1.4395e-01 7.4302e-02 9.7991e-02 1.5860e-01 1.8527e-01 -2.4367e-03 1.6455e-03 -7.6060e-02 -1.5787e-01 9.5785e-02 -1.4475e-01 Enrichment: -11.0716 31.1032 -34.49 200.1957 2.8358 -180.5033 8.1589 -17.8212 -0.8215 36.6882 89.3256 8.3899 27.9093 -49.2889 171.4908 -89.1268 19.5495 -14.4182 56.2434 -60.1011 29.9699 -18.3727 -18.877 -3.1187 13.9159 -81.7845 77.5744 -34.2346 90.4768 -39.8874 76.8186 126.9765 -133.9197 -331.6511 15.8612 -47.6831 22.371 -29.8208 10.7342 30.6966 -34.6434 13.6472 -21.8398 -24.4696 20.0939 31.2976 6.8877 -137.5806 125.9713 -133.4057 51.1913 -72.2183 -10.2195 97.7519 -116.3316 244.9826 -219.7742 -3.5375 165.7984 9.239 13.3775 11.9588 15.5799 12.7472 29.5916 15.301 20.1784 32.4543 39.0456 -3.2842 -3.1906 -1.0007 -0.7192 11.1113 -300.1937 Coefficients: -5.1432e-08 1.4449e-07 -1.6022e-07 9.2999e-07 1.3173e-08 -8.3851e-07 3.7901e-08 -8.2787e-08 -3.8160e-09 1.7043e-07 4.1495e-07 3.8975e-08 1.2965e-07 -2.2897e-07 7.9664e-07 -4.1403e-07 9.0815e-08 -6.6978e-08 2.6127e-07 -2.7919e-07 1.3922e-07 -8.5348e-08 -8.7691e-08 -1.4487e-08 6.4645e-08 -3.7992e-07 3.6036e-07 -1.5903e-07 4.2030e-07 -1.8529e-07 3.5685e-07 5.8986e-07 -6.2211e-07 -1.5407e-06 7.3682e-08 -2.2151e-07 1.0392e-07 -1.3853e-07 4.9865e-08 1.4260e-07 -1.6093e-07 6.3397e-08 -1.0145e-07 -1.1367e-07 9.3344e-08 1.4539e-07 3.1996e-08 -6.3912e-07 5.8519e-07 -6.1972e-07 2.3780e-07 -3.3548e-07 -4.7473e-08 4.5410e-07 -5.4041e-07 1.1380e-06 -1.0209e-06 -1.6433e-08 7.7020e-07 4.2919e-08 6.2144e-08 5.5553e-08 7.2375e-08 5.9216e-08 1.3746e-07 7.1079e-08 9.3737e-08 1.5076e-07 1.8138e-07 -1.5257e-08 -1.4822e-08 -4.6486e-09 -3.3409e-09 5.1617e-08 -1.3945e-06 Coefficient SE: 1.1763e-07 4.5036e-07 1.6224e-07 5.8087e-07 8.3670e-08 8.1543e-07 3.4104e-07 1.7578e-07 7.3106e-08 3.3335e-07 4.4153e-07 1.3079e-07 8.3028e-07 2.9295e-07 3.5960e-07 2.5124e-07 2.6456e-07 1.7002e-07 2.1718e-07 2.1609e-07 2.4097e-07 2.2780e-07 1.2643e-07 1.0124e-07 7.6348e-08 3.4378e-07 2.0149e-07 1.2864e-07 5.0802e-07 1.8870e-07 1.4081e-07 4.6930e-07 4.6033e-07 8.2318e-07 3.2774e-07 8.1976e-07 6.6023e-07 1.4855e-07 1.0922e-07 9.0493e-07 8.9908e-07 1.3558e-07 1.1305e-07 1.5138e-07 7.4069e-08 4.2927e-07 3.4941e-07 7.4425e-07 6.6381e-07 7.4043e-07 3.0316e-07 3.2181e-07 1.8378e-07 1.3869e-06 1.3929e-06 9.9042e-07 8.0053e-07 2.6249e-08 7.9834e-07 2.3507e-08 3.0269e-08 1.9042e-08 4.3335e-08 3.9717e-08 4.6549e-08 2.8026e-08 4.5021e-08 6.4315e-08 5.0778e-08 2.2754e-08 1.7058e-08 4.8032e-09 4.4069e-09 3.5463e-08 1.9839e-06 Lambda GC: 1.3685 Mean Chi^2: 1.6762 Intercept: 1.0391 (0.0327) Ratio: 0.0578 (0.0483)

Genetic Covariance

Total Observed scale gencov: 0.036 (0.0199) Categories: baseL2_0 Coding_UCSCL2_0 Coding_UCSC.extend.500L2_0 Conserved_LindbladTohL2_0 Conserved_LindbladToh.extend.500L2_0 CTCF_HoffmanL2_0 CTCF_Hoffman.extend.500L2_0 DGF_ENCODEL2_0 DGF_ENCODE.extend.500L2_0 DHS_peaks_TrynkaL2_0 DHS_TrynkaL2_0 DHS_Trynka.extend.500L2_0 Enhancer_AnderssonL2_0 Enhancer_Andersson.extend.500L2_0 Enhancer_HoffmanL2_0 Enhancer_Hoffman.extend.500L2_0 FetalDHS_TrynkaL2_0 FetalDHS_Trynka.extend.500L2_0 H3K27ac_HniszL2_0 H3K27ac_Hnisz.extend.500L2_0 H3K27ac_PGC2L2_0 H3K27ac_PGC2.extend.500L2_0 H3K4me1_peaks_TrynkaL2_0 H3K4me1_TrynkaL2_0 H3K4me1_Trynka.extend.500L2_0 H3K4me3_peaks_TrynkaL2_0 H3K4me3_TrynkaL2_0 H3K4me3_Trynka.extend.500L2_0 H3K9ac_peaks_TrynkaL2_0 H3K9ac_TrynkaL2_0 H3K9ac_Trynka.extend.500L2_0 Intron_UCSCL2_0 Intron_UCSC.extend.500L2_0 PromoterFlanking_HoffmanL2_0 PromoterFlanking_Hoffman.extend.500L2_0 Promoter_UCSCL2_0 Promoter_UCSC.extend.500L2_0 Repressed_HoffmanL2_0 Repressed_Hoffman.extend.500L2_0 SuperEnhancer_HniszL2_0 SuperEnhancer_Hnisz.extend.500L2_0 TFBS_ENCODEL2_0 TFBS_ENCODE.extend.500L2_0 Transcr_HoffmanL2_0 Transcr_Hoffman.extend.500L2_0 TSS_HoffmanL2_0 TSS_Hoffman.extend.500L2_0 UTR_3_UCSCL2_0 UTR_3_UCSC.extend.500L2_0 UTR_5_UCSCL2_0 UTR_5_UCSC.extend.500L2_0 WeakEnhancer_HoffmanL2_0 WeakEnhancer_Hoffman.extend.500L2_0 Super_Enhancer_VahediL2_0 Super_Enhancer_Vahedi.extend.500L2_0 Typical_Enhancer_VahediL2_0 Typical_Enhancer_Vahedi.extend.500L2_0 GERP.NSL2_0 GERP.RSsup4L2_0 MAFbin1L2_0 MAFbin2L2_0 MAFbin3L2_0 MAFbin4L2_0 MAFbin5L2_0 MAFbin6L2_0 MAFbin7L2_0 MAFbin8L2_0 MAFbin9L2_0 MAFbin10L2_0 MAF_Adj_Predicted_Allele_AgeL2_0 MAF_Adj_LLD_AFRL2_0 Recomb_Rate_10kbL2_0 Nucleotide_Diversity_10kbL2_0 Backgrd_Selection_StatL2_0 CpG_Content_50kbL2_0 Observed scale gencov: 3.4282e-01 1.8598e-02 -1.1441e-02 4.4061e-02 -2.2418e-02 3.6421e-03 -1.8641e-02 2.4701e-02 -3.6775e-03 -7.8921e-02 9.6974e-02 -1.3534e-01 -5.3028e-03 -4.3672e-03 2.9097e-02 -5.4287e-02 4.3331e-02 1.2781e-02 -4.9092e-02 4.6801e-02 -1.3820e-01 1.2399e-01 -1.1627e-02 -1.3102e-01 1.7895e-01 -2.4283e-02 4.1675e-02 -2.8726e-02 -1.5144e-02 7.6081e-02 -1.4478e-02 6.3289e-01 -6.3880e-01 -4.8746e-03 8.6097e-03 -7.4632e-02 8.0106e-02 -6.7474e-02 -6.6854e-02 6.2667e-02 -4.5573e-02 -3.9057e-03 -1.7353e-02 -2.5565e-02 -6.9331e-02 -2.9339e-03 -2.7576e-03 -2.1816e-02 2.3177e-02 -5.4042e-03 1.4086e-02 2.3231e-02 -3.5723e-02 8.6541e-02 -8.3846e-02 -2.7356e-03 1.0264e-02 -1.3365e-02 -1.7788e-02 -6.3101e-03 9.6732e-03 5.4516e-03 1.1693e-03 3.1908e-03 2.7797e-03 -9.9327e-03 -3.6015e-03 1.6666e-02 2.3764e-03 3.7459e-04 2.1715e-04 -9.1483e-03 -2.1398e-02 -1.9592e-02 -1.3303e-02 Observed scale gencov SE: 1.8683e-01 1.2658e-02 1.7387e-02 1.5582e-02 3.7772e-02 2.1569e-02 2.8113e-02 4.8299e-02 8.6184e-02 5.5379e-02 8.5071e-02 8.8766e-02 6.5882e-03 9.3759e-03 2.5385e-02 3.4818e-02 4.0296e-02 6.2032e-02 1.4613e-01 1.6729e-01 9.6466e-02 1.0679e-01 4.4947e-02 9.4461e-02 9.7656e-02 2.7358e-02 5.1192e-02 5.5559e-02 2.4728e-02 5.0426e-02 5.8111e-02 3.3484e-01 3.4279e-01 9.5102e-03 1.6205e-02 4.1852e-02 4.2777e-02 8.2904e-02 9.8673e-02 2.5055e-01 2.5471e-01 4.0241e-02 6.2758e-02 7.4539e-02 9.3610e-02 1.5024e-02 2.2759e-02 1.2564e-02 1.8037e-02 9.9344e-03 1.3636e-02 1.5171e-02 2.5132e-02 8.5197e-02 8.5980e-02 2.6454e-02 2.7223e-02 5.9425e-02 9.6655e-03 5.3354e-03 6.6214e-03 5.7903e-03 7.4089e-03 6.9964e-03 7.2042e-03 6.2851e-03 7.2370e-03 8.0952e-03 9.2355e-03 4.5577e-04 2.1076e-04 1.8670e-02 3.7735e-02 1.4686e-02 3.9973e-02 Proportion of SNPs: 4.8445e-02 7.1555e-04 3.1543e-03 1.3475e-03 1.6763e-02 1.1579e-03 3.4177e-03 6.9508e-03 2.6809e-02 5.7543e-03 8.6261e-03 2.5012e-02 2.1684e-04 9.4744e-04 2.1176e-03 4.4350e-03 4.3512e-03 1.4325e-02 1.9242e-02 2.0762e-02 1.3264e-02 1.6483e-02 8.7624e-03 2.1535e-02 3.0211e-02 2.0758e-03 6.6003e-03 1.2508e-02 1.9456e-03 6.2853e-03 1.1312e-02 1.8979e-02 1.9436e-02 4.1075e-04 1.5985e-03 1.4750e-03 1.8286e-03 2.2184e-02 3.4809e-02 8.2390e-03 8.3900e-03 6.6140e-03 1.7040e-02 1.6836e-02 3.7150e-02 8.6840e-04 1.6482e-03 5.5728e-04 1.2911e-03 2.6668e-04 1.2925e-03 1.0712e-03 4.3910e-03 1.0122e-03 1.0346e-03 1.0565e-03 1.2630e-03 9.0916e-02 4.3266e-04 3.8185e-03 4.8611e-03 4.8880e-03 4.9477e-03 4.8065e-03 4.8646e-03 4.8560e-03 4.8563e-03 4.8869e-03 4.7449e-03 7.4195e-04 -5.1573e-04 7.6007e-02 2.1951e-01 8.6205e-03 4.8217e-04 Proportion of gencov: 9.5247e+00 5.1673e-01 -3.1788e-01 1.2242e+00 -6.2285e-01 1.0119e-01 -5.1793e-01 6.8629e-01 -1.0218e-01 -2.1927e+00 2.6943e+00 -3.7601e+00 -1.4733e-01 -1.2134e-01 8.0843e-01 -1.5083e+00 1.2039e+00 3.5511e-01 -1.3639e+00 1.3003e+00 -3.8398e+00 3.4448e+00 -3.2303e-01 -3.6402e+00 4.9720e+00 -6.7466e-01 1.1579e+00 -7.9812e-01 -4.2075e-01 2.1138e+00 -4.0224e-01 1.7584e+01 -1.7748e+01 -1.3544e-01 2.3921e-01 -2.0735e+00 2.2256e+00 -1.8747e+00 -1.8575e+00 1.7411e+00 -1.2662e+00 -1.0852e-01 -4.8214e-01 -7.1028e-01 -1.9263e+00 -8.1515e-02 -7.6616e-02 -6.0614e-01 6.4395e-01 -1.5015e-01 3.9136e-01 6.4543e-01 -9.9250e-01 2.4044e+00 -2.3295e+00 -7.6006e-02 2.8517e-01 -3.7133e-01 -4.9421e-01 -1.7532e-01 2.6876e-01 1.5147e-01 3.2488e-02 8.8653e-02 7.7231e-02 -2.7597e-01 -1.0006e-01 4.6303e-01 6.6026e-02 1.0408e-02 6.0333e-03 -2.5417e-01 -5.9452e-01 -5.4435e-01 -3.6960e-01 Enrichment: 196.6105 722.1448 -100.7756 908.4911 -37.1568 87.3915 -151.5432 98.7346 -3.8112 -381.0574 312.341 -150.3357 -679.4449 -128.0679 381.7661 -340.0885 276.6765 24.7885 -70.883 62.6279 -289.4859 208.9932 -36.8659 -169.0375 164.5777 -325.0177 175.4316 -63.8073 -216.2605 336.309 -35.5578 926.5006 -913.1662 -329.7276 149.6492 -1405.7544 1217.1498 -84.5037 -53.3615 211.326 -150.9148 -16.407 -28.2944 -42.1893 -51.8513 -93.8679 -46.4837 -1087.6818 498.7496 -563.0218 302.7931 602.5101 -226.0333 2375.3722 -2251.7123 -71.9407 225.7866 -4.0843 -1142.2597 -45.9123 55.2872 30.9872 6.5664 18.4446 15.8763 -56.8297 -20.6049 94.7492 13.915 14.0273 -11.6986 -3.3441 -2.7084 -63.146 -766.5399 Mean z1*z2: 0.0372 Intercept: 0.0087 (0.0088)

Genetic Correlation

Genetic Correlation: nan (nan) (h2 out of bounds) Z-score: nan (nan) (h2 out of bounds) P: nan (nan) (h2 out of bounds) WARNING: One of the h2's was out of bounds. This usually indicates a data-munging error or that h2 or N is low.

Summary of Genetic Correlation Results p1 p2 rg se z p h2_obs h2_obs_se h2_int h2_int_se gcov_int gcov_int_se Meta_IOP_age_sex_caucasians_MAF0.01_20160806.sumstats.gz vcdr_visit_int.sumstats.gz NA NA NA NA 0.5032 0.0624 1.0391 0.0327 0.0087 0.0088

Analysis finished at Wed May 13 09:22:33 2020 Total time elapsed: 2.0m:44.02s

Here is the log of heritability:

~/Software/S_LDSC/ldsc/ldsc.py --h2 Meta_IOP_age_sex_caucasians_MAF0.01_20160806.sumstats.gz --ref-ld-chr annot_uk10k/baselineLD. --w-ld-chr annot_uk10k/weight.

Beginning analysis at Wed May 13 09:27:34 2020 Reading summary statistics from Meta_IOP_age_sex_caucasians_MAF0.01_20160806.sumstats.gz ... Read summary statistics for 1200645 SNPs. Reading reference panel LD Score from annot_uk10k/baselineLD.[1-22] ... Read reference panel LD Scores for 8743917 SNPs. Removing partitioned LD Scores with zero variance. Reading regression weight LD Score from annot_uk10k/weight.[1-22] ... Read regression weight LD Scores for 8743917 SNPs. After merging with reference panel LD, 1164815 SNPs remain. After merging with regression SNP LD, 1164815 SNPs remain. Removed 0 SNPs with chi^2 > 80 (1164815 SNPs remain) Total Observed scale h2: 0.12 (0.0297) Categories: baseL2_0 Coding_UCSCL2_0 Coding_UCSC.extend.500L2_0 Conserved_LindbladTohL2_0 Conserved_LindbladToh.extend.500L2_0 CTCF_HoffmanL2_0 CTCF_Hoffman.extend.500L2_0 DGF_ENCODEL2_0 DGF_ENCODE.extend.500L2_0 DHS_peaks_TrynkaL2_0 DHS_TrynkaL2_0 DHS_Trynka.extend.500L2_0 Enhancer_AnderssonL2_0 Enhancer_Andersson.extend.500L2_0 Enhancer_HoffmanL2_0 Enhancer_Hoffman.extend.500L2_0 FetalDHS_TrynkaL2_0 FetalDHS_Trynka.extend.500L2_0 H3K27ac_HniszL2_0 H3K27ac_Hnisz.extend.500L2_0 H3K27ac_PGC2L2_0 H3K27ac_PGC2.extend.500L2_0 H3K4me1_peaks_TrynkaL2_0 H3K4me1_TrynkaL2_0 H3K4me1_Trynka.extend.500L2_0 H3K4me3_peaks_TrynkaL2_0 H3K4me3_TrynkaL2_0 H3K4me3_Trynka.extend.500L2_0 H3K9ac_peaks_TrynkaL2_0 H3K9ac_TrynkaL2_0 H3K9ac_Trynka.extend.500L2_0 Intron_UCSCL2_0 Intron_UCSC.extend.500L2_0 PromoterFlanking_HoffmanL2_0 PromoterFlanking_Hoffman.extend.500L2_0 Promoter_UCSCL2_0 Promoter_UCSC.extend.500L2_0 Repressed_HoffmanL2_0 Repressed_Hoffman.extend.500L2_0 SuperEnhancer_HniszL2_0 SuperEnhancer_Hnisz.extend.500L2_0 TFBS_ENCODEL2_0 TFBS_ENCODE.extend.500L2_0 Transcr_HoffmanL2_0 Transcr_Hoffman.extend.500L2_0 TSS_HoffmanL2_0 TSS_Hoffman.extend.500L2_0 UTR_3_UCSCL2_0 UTR_3_UCSC.extend.500L2_0 UTR_5_UCSCL2_0 UTR_5_UCSC.extend.500L2_0 WeakEnhancer_HoffmanL2_0 WeakEnhancer_Hoffman.extend.500L2_0 Super_Enhancer_VahediL2_0 Super_Enhancer_Vahedi.extend.500L2_0 Typical_Enhancer_VahediL2_0 Typical_Enhancer_Vahedi.extend.500L2_0 GERP.NSL2_0 GERP.RSsup4L2_0 MAFbin1L2_0 MAFbin2L2_0 MAFbin3L2_0 MAFbin4L2_0 MAFbin5L2_0 MAFbin6L2_0 MAFbin7L2_0 MAFbin8L2_0 MAFbin9L2_0 MAFbin10L2_0 MAF_Adj_Predicted_Allele_AgeL2_0 MAF_Adj_LLD_AFRL2_0 Recomb_Rate_10kbL2_0 Nucleotide_Diversity_10kbL2_0 Backgrd_Selection_StatL2_0 CpG_Content_50kbL2_0 Observed scale h2: 1.3970e-01 2.5312e-03 -1.0244e-02 6.3822e-02 -9.6088e-02 2.9231e-02 -3.6625e-02 5.6407e-02 3.9184e-03 8.5948e-04 -9.2934e-02 1.3990e-02 -1.0748e-02 8.7392e-03 -4.8455e-03 -1.4042e-02 8.7198e-02 4.3818e-02 -3.5685e-01 3.5167e-01 3.0131e-02 3.9479e-02 -9.5358e-02 1.5817e-01 -1.9778e-01 -8.1964e-02 1.2208e-01 -5.8997e-02 3.1198e-02 1.9116e-01 -1.7228e-01 1.0672e+00 -1.0861e+00 1.1958e-02 -1.2926e-02 -1.0423e-02 -2.5490e-03 -7.9917e-02 -9.1906e-02 1.3531e-01 -1.0827e-01 5.6881e-03 1.1313e-02 -5.3251e-02 -3.9593e-02 6.7042e-03 -5.9198e-02 7.2285e-03 -5.2404e-03 -6.1200e-05 1.4031e-02 -3.9059e-02 7.9460e-03 5.0045e-03 -9.9788e-03 -7.0207e-03 -6.0298e-03 6.0377e-03 2.2073e-02 2.6213e-03 6.8182e-03 1.4579e-02 1.3273e-02 1.4235e-02 1.2448e-02 6.9221e-03 1.1185e-02 9.0887e-03 2.2018e-02 -1.0069e-04 2.7207e-04 8.6732e-03 2.0047e-02 5.2701e-02 9.0944e-02 Observed scale h2 SE: 2.2910e-01 1.7639e-02 2.5491e-02 2.8823e-02 6.8440e-02 3.0973e-02 3.8577e-02 8.1296e-02 1.3517e-01 8.8480e-02 1.0997e-01 1.4523e-01 1.1429e-02 1.8939e-02 3.9339e-02 5.0978e-02 6.5246e-02 9.5935e-02 2.5005e-01 2.7438e-01 1.4845e-01 1.6461e-01 7.7134e-02 1.5704e-01 1.6714e-01 3.4156e-02 6.9643e-02 8.3300e-02 3.8510e-02 8.3093e-02 8.8692e-02 5.8052e-01 5.9472e-01 1.4018e-02 2.1657e-02 5.5392e-02 5.8455e-02 1.2092e-01 1.3947e-01 3.4472e-01 3.4626e-01 1.1520e-01 1.2587e-01 8.3290e-02 1.2691e-01 2.3491e-02 3.1898e-02 1.5097e-02 1.5845e-02 1.0821e-02 1.4844e-02 2.5445e-02 3.7264e-02 1.1911e-01 1.2019e-01 3.6453e-02 4.0936e-02 9.0654e-02 1.7302e-02 7.5618e-03 1.0623e-02 8.9505e-03 1.0930e-02 9.1175e-03 1.1464e-02 9.4041e-03 8.7965e-03 1.0322e-02 8.8154e-03 6.9584e-04 2.9470e-04 2.7222e-02 4.8196e-02 2.1892e-02 5.9942e-02 Proportion of SNPs: 4.8445e-02 7.1555e-04 3.1543e-03 1.3475e-03 1.6763e-02 1.1579e-03 3.4177e-03 6.9508e-03 2.6809e-02 5.7543e-03 8.6261e-03 2.5012e-02 2.1684e-04 9.4744e-04 2.1176e-03 4.4350e-03 4.3512e-03 1.4325e-02 1.9242e-02 2.0762e-02 1.3264e-02 1.6483e-02 8.7624e-03 2.1535e-02 3.0211e-02 2.0758e-03 6.6003e-03 1.2508e-02 1.9456e-03 6.2853e-03 1.1312e-02 1.8979e-02 1.9436e-02 4.1075e-04 1.5985e-03 1.4750e-03 1.8286e-03 2.2184e-02 3.4809e-02 8.2390e-03 8.3900e-03 6.6140e-03 1.7040e-02 1.6836e-02 3.7150e-02 8.6840e-04 1.6482e-03 5.5728e-04 1.2911e-03 2.6668e-04 1.2925e-03 1.0712e-03 4.3910e-03 1.0122e-03 1.0346e-03 1.0565e-03 1.2630e-03 9.0916e-02 4.3266e-04 3.8185e-03 4.8611e-03 4.8880e-03 4.9477e-03 4.8065e-03 4.8646e-03 4.8560e-03 4.8563e-03 4.8869e-03 4.7449e-03 7.4195e-04 -5.1573e-04 7.6007e-02 2.1951e-01 8.6205e-03 4.8217e-04 Proportion of h2g: 1.1639e+00 2.1089e-02 -8.5350e-02 5.3175e-01 -8.0058e-01 2.4354e-01 -3.0515e-01 4.6997e-01 3.2647e-02 7.1609e-03 -7.7431e-01 1.1656e-01 -8.9549e-02 7.2813e-02 -4.0372e-02 -1.1700e-01 7.2652e-01 3.6508e-01 -2.9732e+00 2.9300e+00 2.5104e-01 3.2893e-01 -7.9450e-01 1.3179e+00 -1.6479e+00 -6.8291e-01 1.0171e+00 -4.9155e-01 2.5993e-01 1.5927e+00 -1.4354e+00 8.8915e+00 -9.0491e+00 9.9628e-02 -1.0770e-01 -8.6841e-02 -2.1238e-02 -6.6585e-01 -7.6574e-01 1.1274e+00 -9.0204e-01 4.7392e-02 9.4257e-02 -4.4367e-01 -3.2988e-01 5.5858e-02 -4.9322e-01 6.0226e-02 -4.3662e-02 -5.0990e-04 1.1690e-01 -3.2543e-01 6.6204e-02 4.1696e-02 -8.3141e-02 -5.8495e-02 -5.0239e-02 5.0304e-02 1.8391e-01 2.1840e-02 5.6807e-02 1.2147e-01 1.1059e-01 1.1860e-01 1.0371e-01 5.7673e-02 9.3193e-02 7.5725e-02 1.8345e-01 -8.3893e-04 2.2668e-03 7.2263e-02 1.6703e-01 4.3909e-01 7.5773e-01 Enrichment: 2.4026e+01 2.9472e+01 -2.7058e+01 3.9462e+02 -4.7759e+01 2.1033e+02 -8.9285e+01 6.7613e+01 1.2178e+00 1.2445e+00 -8.9763e+01 4.6603e+00 -4.1297e+02 7.6852e+01 -1.9065e+01 -2.6380e+01 1.6697e+02 2.5485e+01 -1.5452e+02 1.4112e+02 1.8926e+01 1.9956e+01 -9.0672e+01 6.1197e+01 -5.4545e+01 -3.2899e+02 1.5411e+02 -3.9298e+01 1.3360e+02 2.5341e+02 -1.2689e+02 4.6849e+02 -4.6558e+02 2.4255e+02 -6.7374e+01 -5.8874e+01 -1.1615e+01 -3.0014e+01 -2.1998e+01 1.3684e+02 -1.0751e+02 7.1653e+00 5.5315e+00 -2.6353e+01 -8.8797e+00 6.4323e+01 -2.9924e+02 1.0807e+02 -3.3817e+01 -1.9120e+00 9.0444e+01 -3.0379e+02 1.5077e+01 4.1192e+01 -8.0363e+01 -5.5366e+01 -3.9777e+01 5.5330e-01 4.2506e+02 5.7195e+00 1.1686e+01 2.4850e+01 2.2352e+01 2.4675e+01 2.1320e+01 1.1877e+01 1.9190e+01 1.5495e+01 3.8662e+01 -1.1307e+00 -4.3954e+00 9.5074e-01 7.6091e-01 5.0936e+01 1.5715e+03 Coefficients: 2.6622e-08 3.2657e-08 -2.9982e-08 4.3726e-07 -5.2920e-08 2.3306e-07 -9.8932e-08 7.4918e-08 1.3493e-09 1.3789e-09 -9.9462e-08 5.1639e-09 -4.5759e-07 8.5156e-08 -2.1125e-08 -2.9231e-08 1.8501e-07 2.8238e-08 -1.7121e-07 1.5637e-07 2.0971e-08 2.2112e-08 -1.0047e-07 6.7809e-08 -6.0439e-08 -3.6454e-07 1.7076e-07 -4.3544e-08 1.4804e-07 2.8079e-07 -1.4060e-07 5.1911e-07 -5.1589e-07 2.6876e-07 -7.4654e-08 -6.5235e-08 -1.2870e-08 -3.3257e-08 -2.4375e-08 1.5162e-07 -1.1913e-07 7.9395e-09 6.1292e-09 -2.9201e-08 -9.8392e-09 7.1273e-08 -3.3158e-07 1.1975e-07 -3.7471e-08 -2.1186e-09 1.0022e-07 -3.3661e-07 1.6706e-08 4.5643e-08 -8.9046e-08 -6.1348e-08 -4.4075e-08 6.1309e-10 4.7099e-07 6.3374e-09 1.2949e-08 2.7535e-08 2.4767e-08 2.7341e-08 2.3624e-08 1.3160e-08 2.1264e-08 1.7170e-08 4.2840e-08 -1.2529e-09 -4.8704e-09 1.0535e-09 8.4312e-10 5.6439e-08 1.7413e-06 Coefficient SE: 4.3658e-08 2.2758e-07 7.4607e-08 1.9747e-07 3.7693e-08 2.4695e-07 1.0421e-07 1.0798e-07 4.6547e-08 1.4195e-07 1.1769e-07 5.3605e-08 4.8659e-07 1.8454e-07 1.7150e-07 1.0612e-07 1.3843e-07 6.1825e-08 1.1997e-07 1.2200e-07 1.0332e-07 9.2199e-08 8.1268e-08 6.7325e-08 5.1077e-08 1.5191e-07 9.7412e-08 6.1481e-08 1.8274e-07 1.2205e-07 7.2381e-08 2.8238e-07 2.8249e-07 3.1506e-07 1.2508e-07 3.4669e-07 2.9513e-07 5.0322e-08 3.6991e-08 3.8626e-07 3.8101e-07 1.6080e-07 6.8195e-08 4.5673e-08 3.1538e-08 2.4974e-07 1.7866e-07 2.5010e-07 1.1330e-07 3.7460e-07 1.0603e-07 2.1928e-07 7.8348e-08 1.0864e-06 1.0725e-06 3.1853e-07 2.9922e-07 9.2054e-09 3.6918e-07 1.8282e-08 2.0175e-08 1.6905e-08 2.0394e-08 1.7512e-08 2.1756e-08 1.7879e-08 1.6723e-08 1.9500e-08 1.7152e-08 8.6583e-09 5.2754e-09 3.3064e-09 2.0270e-09 2.3445e-08 1.1477e-06 Lambda GC: 1.0772 Mean Chi^2: 1.0929 Intercept: 1.0219 (0.01) Ratio: 0.2354 (0.1076) Analysis finished at Wed May 13 09:29:55 2020 Total time elapsed: 2.0m:20.69s

abbynewbury commented 5 months ago

Hi, I wanted to check if a solution was ever found for this issue? I am experiencing the same thing. Thanks!

aksarkar commented 5 months ago

@abbynewbury The basic issue is that when computing genetic correlations, only SNPs with data present in both studies are used.

I am unsure what is happening if one gets a nonsense heritability estimate for that subset of SNPs (as opposed to a slightly different estimate).