Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_plot

beta_std plot

beta_std_plot

Metadata

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}
 

LDSC

*********************************************************************
* 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 /data/cromwell-executions/qc/5e294b2a-d116-4b0c-8693-ed79a88f0d1a/call-ldsc/inputs/-261044388/ieu-b-4860.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4860/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Wed Jan  5 19:34:04 2022
Reading summary statistics from /data/cromwell-executions/qc/5e294b2a-d116-4b0c-8693-ed79a88f0d1a/call-ldsc/inputs/-261044388/ieu-b-4860.vcf.gz ...
Read summary statistics for 7986977 SNPs.
Dropped 39184 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1202971 SNPs remain.
After merging with regression SNP LD, 1202971 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0119 (0.0063)
Lambda GC: 1.0536
Mean Chi^2: 1.0477
Intercept: 1.0299 (0.0068)
Ratio: 0.6266 (0.1434)
Analysis finished at Wed Jan  5 19:35:45 2022
Total time elapsed: 1.0m:40.92s

QC metrics

Metrics

Metrics

{
    "af_correlation": "NA",
    "inflation_factor": 1.0388,
    "mean_EFFECT": -0,
    "n": 78007,
    "n_snps": 7987053,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 285767,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 7987053,
    "n_miss_AF_reference": 166434,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1202971,
    "ldsc_nsnp_merge_regression_ld": 1202971,
    "ldsc_observed_scale_h2_beta": 0.0119,
    "ldsc_observed_scale_h2_se": 0.0063,
    "ldsc_intercept_beta": 1.0299,
    "ldsc_intercept_se": 0.0068,
    "ldsc_lambda_gc": 1.0536,
    "ldsc_mean_chisq": 1.0477,
    "ldsc_ratio": 0.6268
}
 

Flags

name value
af_correlation NA
inflation_factor FALSE
n FALSE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio TRUE
ldsc_intercept_beta FALSE
n_clumped_hits FALSE
r2_sum1 FALSE
r2_sum2 FALSE
r2_sum3 FALSE
r2_sum4 FALSE

Definitions

General metrics

  • af_correlation: Correlation coefficient between AF and AF_reference.
  • inflation_factor (lambda): Genomic inflation factor.
  • mean_EFFECT: Mean of EFFECT size.
  • n: Maximum value of reported sample size across all SNPs, \(n\).
  • n_clumped_hits: Number of clumped hits.
  • n_snps: Number of SNPs
  • n_p_sig: Number of SNPs with pvalue below 5e-8.
  • n_mono: Number of monomorphic (MAF == 1 or MAF == 0) SNPs.
  • n_ns: Number of SNPs with nonsense values:
    • alleles other than A, C, G or T.
    • P-values < 0 or > 1.
    • negative or infinite standard errors (<= 0 or = Infinity).
    • infinite beta estimates or allele frequencies < 0 or > 1.
  • n_mac: Number of cases where MAC (\(2 \times N \times MAF\)) is less than 6.
  • is_snpid_unique: true if the combination of ID REF ALT is unique and therefore no duplication in snpid.
  • n_miss_<*>: Number of NA observations for <*> column.

se_n metrics

  • n_est: Estimated sample size value, \(\widehat{n}\).
  • ratio_se_n: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). We expect ratio_se_n to be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.
  • mean_diff: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.
    • \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
    • \({z}_j = \frac{\beta_j}{{se}_j}\),
    • and \(\beta_j\) is the reported effect size.
  • ratio_diff: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff and the mean of diff2 (expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.
    • \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
    • \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
  • sd_y_est1: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.
    • \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
    • \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
    • and \({se}_j\) is the reported standard error.
  • sd_y_est2: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.
    • \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
    • \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),

r2 metrics

Sum of variance explained, calculated from the clumped top hits sample.

  • r2_sum<*>: r2 statistics under various assumptions
    • 1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).
    • 2: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),
    • 3: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),
    • 4: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).

LDSC metrics

Metrics from LD regression

  • ldsc_nsnp_merge_refpanel_ld: Number of remaining SNPs after merging with reference panel LD.
  • ldsc_nsnp_merge_regression_ld: Number of remaining SNPs after merging with regression SNP LD.
  • ldsc_observed_scale_h2_{beta,se} Coefficient value and SE for total observed scale h2.
  • ldsc_intercept_{beta,se}: Coefficient value and SE for intercept. Intercept is expected to be 1.
  • ldsc_lambda_gc: Lambda GC statistics.
  • ldsc_mean_chisq: Mean \(\chi^2\) statistics.
  • ldsc_ratio: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher \(h^2\) per SNP).

Flags

When a metric needs attention, the flag should return TRUE.

  • af_correlation: abs(af_correlation) < 0.7.
  • inflation_factor: inflation_factor > 1.2.
  • n: n (max reported sample size) < 10000.
  • is_snpid_non_unique: NOT is_snpid_unique.
  • mean_EFFECT_nonfinite: mean(EFFECT) is NA, NaN, or Inf.
  • mean_EFFECT_05: abs(mean(EFFECT)) > 0.5.
  • mean_EFFECT_01: abs(mean(EFFECT)) > 0.1.
  • mean_chisq: ldsc_mean_chisq > 1.3 or ldsc_mean_chisq < 0.7.
  • n_p_sig: n_p_sig > 1000.
  • miss_<*>: n_miss_<*> / n_snps > 0.01.
  • ldsc_ratio: ldsc_ratio > 0.5
  • ldsc_intercept_beta: ldsc_intercept_beta > 1.5
  • n_clumped_hits: n_clumped_hits > 1000
  • r2_sum<*>: r2_sum<*> > 0.5

Plots

  • Manhattan plot
    • Red line: \(-log_{10}^{5 \times 10^{-8}}\)
    • Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
  • QQ plot
  • AF plot
  • P-Z plot
  • beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)

Diagnostics

Details

Summary stats

skim_type skim_variable n_missing complete_rate character.min character.max character.empty character.n_unique character.whitespace logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 26 0.9999967 3 58 0 7986884 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 43 0 16651 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 44 0 6034 0 NA NA NA NA NA NA NA NA NA NA
logical AF 7987053 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.646238e+00 5.754043e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.884892e+07 5.635741e+07 3.0200e+02 3.246384e+07 6.941758e+07 1.146302e+08 2.492223e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -1.370000e-05 5.117500e-03 -5.2800e-02 -2.500000e-03 0.000000e+00 2.500000e-03 4.710000e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 4.379300e-03 2.463800e-03 2.2000e-03 2.500000e-03 3.300000e-03 5.600000e-03 1.370000e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.933516e-01 2.904518e-01 1.0000e-07 2.397000e-01 4.918005e-01 7.446994e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.934946e-01 2.905267e-01 1.0000e-07 2.404299e-01 4.904111e-01 7.456925e-01 1.000000e+00 ▇▇▇▇▇
numeric AF_reference 166434 0.9791620 NA NA NA NA NA NA NA 2.642209e-01 2.522116e-01 0.0000e+00 5.670930e-02 1.783150e-01 4.125400e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA NA NA 7.361196e+04 5.964515e+03 4.7002e+04 7.328200e+04 7.674700e+04 7.800700e+04 7.800700e+04 ▁▁▂▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 797440 rs58013264 T C -0.0008 0.0036 0.8233000 0.8241409 NA 0.189497 68094
1 798400 rs10900604 A G 0.0008 0.0030 0.7842003 0.7897258 NA 0.410543 68094
1 798959 rs11240777 G A 0.0009 0.0029 0.7459007 0.7562987 NA 0.409944 70768
1 801467 rs61768212 G C -0.0007 0.0036 0.8483001 0.8458279 NA 0.193091 68094
1 804759 rs7526310 C T -0.0009 0.0036 0.8100000 0.8025873 NA 0.193890 68094
1 808223 rs4951933 G C 0.0010 0.0031 0.7393992 0.7470129 NA 0.452077 62455
1 808631 rs11240779 G A 0.0003 0.0029 0.9305999 0.9176072 NA 0.453474 68094
1 808928 rs11240780 C T 0.0002 0.0029 0.9434001 0.9450171 NA 0.452276 68094
1 845274 rs112856858 G T 0.0017 0.0032 0.5863001 0.5952455 NA 0.374002 62455
1 845635 rs117086422 C T 0.0012 0.0029 0.6676994 0.6790256 NA 0.158546 70768
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51218377 rs2519461 G C -0.0017 0.0051 0.7467995 0.7388827 NA 0.0826677 52190
22 51219006 rs28729663 G A -0.0070 0.0041 0.0845805 0.0877631 NA 0.2052720 49516
22 51219387 rs9616832 T C -0.0021 0.0051 0.6766997 0.6805119 NA 0.0654952 52190
22 51219704 rs147475742 G A -0.0102 0.0071 0.1540001 0.1508261 NA 0.0473243 49516
22 51221190 rs369304721 G A -0.0111 0.0063 0.0785597 0.0780854 NA NA 49516
22 51221731 rs115055839 T C -0.0023 0.0052 0.6560002 0.6582666 NA 0.0625000 52190
22 51222100 rs114553188 G T -0.0098 0.0058 0.0896107 0.0910939 NA 0.0880591 52190
22 51223637 rs375798137 G A -0.0102 0.0058 0.0791899 0.0786420 NA 0.0788738 52190
22 51229805 rs9616985 T C -0.0019 0.0052 0.7142003 0.7148243 NA 0.0730831 52190
22 51237063 rs3896457 T C -0.0010 0.0031 0.7362003 0.7470129 NA 0.2050720 49516

bcf preview

1   797440  rs58013264  T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.0008:0.0036:0.0844419:68094:rs58013264
1   798400  rs10900604  A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0008:0.003:0.105573:68094:rs10900604
1   798959  rs11240777  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0009:0.0029:0.127319:70768:rs11240777
1   801467  rs61768212  G   C   .   PASS    .   ES:SE:LP:SS:ID  -0.0007:0.0036:0.0714505:68094:rs61768212
1   804759  rs7526310   C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.0009:0.0036:0.091515:68094:rs7526310
1   808223  rs1557576983    G   C   .   PASS    .   ES:SE:LP:SS:ID  0.001:0.0031:0.131121:62455:rs1557576983
1   808631  rs11240779  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0003:0.0029:0.031237:68094:rs11240779
1   808928  rs1247187939    C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0002:0.0029:0.0253041:68094:rs1247187939
1   845274  rs1324283754    G   T   .   PASS    .   ES:SE:LP:SS:ID  0.0017:0.0032:0.23188:62455:rs1324283754
1   845635  rs117086422 C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0012:0.0029:0.175419:70768:rs117086422
1   845938  rs57760052  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0011:0.0029:0.147093:70768:rs57760052
1   846078  rs778265812 C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0023:0.003:0.360215:70768:rs778265812
1   846398  rs58781670  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0003:0.0029:0.0420098:70768:rs58781670
1   846465  rs60454217  C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.0142:0.0092:0.915781:68094:rs60454217
1   846543  rs79396034  G   T   .   PASS    .   ES:SE:LP:SS:ID  -0.0125:0.0095:0.726536:68094:rs79396034
1   846808  rs4475691   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0021:0.003:0.323124:70768:rs4475691
1   846864  rs1269142199    G   C   .   PASS    .   ES:SE:LP:SS:ID  0.0022:0.003:0.342275:70768:rs1269142199
1   847228  rs3905286   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0009:0.0029:0.116566:70768:rs3905286
1   847491  rs1158719307    G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0028:0.0029:0.486516:70768:rs1158719307
1   848090  rs4246505   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.003:0.0029:0.524619:70768:rs4246505
1   848445  rs1156895099    G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0027:0.0029:0.454817:70768:rs1156895099
1   848456  rs11507767  A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0028:0.0029:0.467373:70768:rs11507767
1   848738  rs3829741   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.003:0.0029:0.520281:70768:rs3829741
1   850062  rs28723578  A   T   .   PASS    .   ES:SE:LP:SS:ID  0.0027:0.0029:0.45705:70768:rs28723578
1   850123  rs28622257  C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0029:0.0029:0.501001:70768:rs28622257
1   851190  rs28609852  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0026:0.0029:0.443336:70768:rs28609852
1   851204  rs28552953  G   C   .   PASS    .   ES:SE:LP:SS:ID  0.0029:0.0028:0.507938:70768:rs28552953
1   852664  rs28605311  C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0033:0.0029:0.593801:70768:rs28605311
1   852758  rs4970462   G   C   .   PASS    .   ES:SE:LP:SS:ID  0.0032:0.0029:0.571379:70768:rs4970462
1   853239  rs4970380   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0033:0.0029:0.579055:70768:rs4970380
1   853805  rs3748591   C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.0149:0.0083:1.13071:68094:rs3748591
1   854250  rs7537756   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0028:0.0029:0.483332:70768:rs7537756
1   854429  rs72902552  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0152:0.0083:1.17076:68094:rs72902552
1   856436  rs34105146  TG  T   .   PASS    .   ES:SE:LP:SS:ID  0.0048:0.0032:0.872247:62455:rs34105146
1   856476  rs4040605   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0042:0.0025:1.00436:68094:rs4040605
1   857177  rs386627408 T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.014:0.0081:1.07816:68094:rs386627408
1   858040  rs4970460   C   A   .   PASS    .   ES:SE:LP:SS:ID  0.0036:0.003:0.646084:68094:rs4970460
1   858051  rs4970459   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0038:0.003:0.68382:68094:rs4970459
1   858801  rs7418179   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.0012:0.0029:0.175549:68094:rs7418179
1   859404  rs71509444  C   G   .   PASS    .   ES:SE:LP:SS:ID  0.0105:0.009:0.607655:62455:rs71509444
1   859685  rs111572704 G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0032:0.0031:0.508778:62455:rs111572704
1   859690  rs71509445  C   G   .   PASS    .   ES:SE:LP:SS:ID  0.014:0.0095:0.848018:62455:rs71509445
1   859701  rs71509446  C   G   .   PASS    .   ES:SE:LP:SS:ID  0.014:0.0095:0.848018:62455:rs71509446
1   859913  rs1187056171    A   G   .   PASS    .   ES:SE:LP:SS:ID  0.02:0.0089:1.6038:68094:rs1187056171
1   860416  rs61464428  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0015:0.0029:0.225775:68094:rs61464428
1   860461  rs57465118  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0149:0.0079:1.21645:68094:rs57465118
1   860521  rs57924093  C   A   .   PASS    .   ES:SE:LP:SS:ID  0.0149:0.0079:1.21645:68094:rs57924093
1   860688  rs60837925  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0015:0.0029:0.221053:68094:rs60837925
1   860854  rs57816555  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0088:0.0103:0.402963:62455:rs57816555
1   861008  rs28521172  G   C   .   PASS    .   ES:SE:LP:SS:ID  0.0151:0.0079:1.24094:68094:rs28521172