Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std 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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-98/ieu-a-98.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-98/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 20:58:29 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-98/ieu-a-98.vcf.gz ...
Read summary statistics for 2724231 SNPs.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1271677 SNPs remain.
After merging with regression SNP LD, 1271677 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1333 (0.0137)
Lambda GC: 1.0073
Mean Chi^2: 1.0228
Intercept: 0.9478 (0.0047)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb  4 20:59:01 2020
Total time elapsed: 32.53s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9172,
    "inflation_factor": 1,
    "mean_EFFECT": 0.0001,
    "n": 32851,
    "n_snps": 2724231,
    "n_clumped_hits": 2,
    "n_p_sig": 58,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 464663,
    "n_miss_AF_reference": 26376,
    "n_est": 35432.3143,
    "ratio_se_n": 1.0385,
    "mean_diff": 2.1877e-06,
    "ratio_diff": 0.5275,
    "sd_y_est1": 1.0409,
    "sd_y_est2": 1.081,
    "r2_sum1": 0.0027,
    "r2_sum2": 0.0025,
    "r2_sum3": 0.0023,
    "r2_sum4": 0.0023,
    "ldsc_nsnp_merge_refpanel_ld": 1271677,
    "ldsc_nsnp_merge_regression_ld": 1271677,
    "ldsc_observed_scale_h2_beta": 0.1333,
    "ldsc_observed_scale_h2_se": 0.0137,
    "ldsc_intercept_beta": 0.9478,
    "ldsc_intercept_se": 0.0047,
    "ldsc_lambda_gc": 1.0073,
    "ldsc_mean_chisq": 1.0228,
    "ldsc_ratio": -2.2895
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique FALSE
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 FALSE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 42 0 2724231 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.614108e+00 5.687595e+00 1.0000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.881034e+07 5.589149e+07 6689.0000 3.245769e+07 7.000840e+07 1.144217e+08 2.492114e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.359000e-04 1.127292e+00 -500.0000 -8.700000e-03 0.000000e+00 8.700000e-03 1.000000e+03 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.817840e-02 1.177269e+00 0.0082 9.000000e-03 1.100000e-02 1.700000e-02 1.000000e+03 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.983244e-01 2.897084e-01 0.0000 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.984688e-01 2.897026e-01 0.0000 2.469070e-01 4.992466e-01 7.492810e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 464663 0.8294333 NA NA NA NA NA 3.565768e-01 2.754925e-01 0.0083 1.167000e-01 2.917000e-01 5.583000e-01 9.917000e-01 ▇▅▃▂▂
numeric AF_reference 26376 0.9903180 NA NA NA NA NA 3.550166e-01 2.607435e-01 0.0000 1.353830e-01 2.899360e-01 5.415340e-01 1.000000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 2.941823e+04 8.396040e+03 118.0000 3.156940e+04 3.284140e+04 3.284810e+04 3.285100e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 564477 rs6650104 A G -0.0250 0.220 0.9100000 0.9095261 NA 0.0003994 611.86
1 721290 rs12565286 G C 0.0160 0.033 0.6200004 0.6277838 NA 0.0371406 13620.00
1 723819 rs11804171 T A 0.0170 0.033 0.6100002 0.6064471 NA 0.1345850 13634.00
1 723891 rs2977670 G C 0.0050 0.045 0.9100000 0.9115282 NA 0.7799520 7115.00
1 752566 rs3094315 G A -0.0025 0.013 0.8499999 0.8475012 NA 0.7182510 22271.00
1 752721 rs3131972 A G -0.0490 0.073 0.5000000 0.5020722 NA 0.6533550 611.91
1 753541 rs2073813 G A -0.0170 0.020 0.3900004 0.3953251 NA 0.3019170 14345.00
1 754182 rs3131969 A G -0.0190 0.076 0.8000000 0.8025873 NA 0.6785140 611.97
1 754192 rs3131968 A G -0.0170 0.023 0.4600002 0.4598278 NA 0.6785140 9167.75
1 760912 rs1048488 C T -0.0360 0.074 0.6200004 0.6266223 NA 0.7340260 611.97
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51211392 rs3888396 T C -0.0089 0.0470 0.8499999 0.8498093 NA 0.1641370 8149.0
22 51212875 rs2238837 A C 0.0031 0.0140 0.8300000 0.8247587 0.3917 0.3724040 20750.6
22 51213613 rs34726907 C T -0.0660 0.0520 0.2099999 0.2043588 NA 0.1727240 1860.0
22 51219006 rs28729663 G A -0.0800 0.0470 0.0890000 0.0887314 NA 0.2052720 1990.0
22 51229805 rs9616985 T C -0.0019 0.0300 0.9500000 0.9495011 0.0917 0.0730831 18609.9
23 35921591 rs2204667 C G -0.0150 0.0110 0.1800002 0.1726820 0.1667 NA 32844.2
23 51666786 rs14115 A G -0.0098 0.0180 0.5900000 0.5861357 0.0250 NA 32762.8
23 70163799 rs1626496 A C -0.0170 0.0170 0.2999998 0.3173105 0.0750 NA 32850.0
23 91415872 rs6562597 G A -0.0130 0.0330 0.6999999 0.6936258 0.0083 0.0021192 30944.3
23 118495837 rs12882977 G A 0.0022 0.0084 0.7899998 0.7933949 0.5167 0.2307280 32847.4

bcf preview

1   564477  rs6650104   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.025:0.22:0.0409586:611.86:rs6650104
1   721290  rs12565286  G   C   .   PASS    .   ES:SE:LP:SS:ID  0.016:0.033:0.207608:13620:rs12565286
1   723819  rs11804171  T   A   .   PASS    .   ES:SE:LP:SS:ID  0.017:0.033:0.21467:13634:rs11804171
1   723891  rs2977670   G   C   .   PASS    .   ES:SE:LP:SS:ID  0.005:0.045:0.0409586:7115:rs2977670
1   752566  rs3094315   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0025:0.013:0.0705811:22271:rs3094315
1   752721  rs3131972   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.049:0.073:0.30103:611.91:rs3131972
1   753541  rs2073813   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.017:0.02:0.408935:14345:rs2073813
1   754182  rs3131969   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.019:0.076:0.09691:611.97:rs3131969
1   754192  rs3131968   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.017:0.023:0.337242:9167.75:rs3131968
1   760912  rs1048488   C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.036:0.074:0.207608:611.97:rs1048488
1   761732  rs2286139   C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.07:0.045:0.958607:1975:rs2286139
1   768448  rs12562034  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.022:0.027:0.387216:13211:rs12562034
1   775659  rs2905035   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0012:0.015:0.0268721:23511.7:rs2905035
1   776546  rs12124819  A   G   .   PASS    .   ES:SE:LP:SS:ID  0.036:0.026:0.769551:4760.41:rs12124819
1   777122  rs2980319   A   T   .   PASS    .   ES:SE:LP:SS:ID  -0.0002:0.015:0.00436481:23512.6:rs2980319
1   779322  rs4040617   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.0012:0.015:0.0268721:22771.2:rs4040617
1   780785  rs2977612   T   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0005:0.015:0.0132283:23511.6:rs2977612
1   784023  rs17160939  A   G   .   PASS    .   ES:SE:LP:SS:ID  0.22:0.12:1.24413:2857.98:rs17160939
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0012:0.015:0.0268721:23511.5:rs2905062
1   785989  rs2980300   T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0035:0.015:0.0861861:23439.5:rs2980300
1   798026  rs4951864   C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.014:0.027:0.229148:13211.5:rs4951864
1   798801  rs12132517  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.018:0.027:0.309804:13176.3:rs12132517
1   798959  rs11240777  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.013:0.017:0.346787:14707.9:rs11240777
1   838555  rs4970383   C   A   .   PASS    .   ES:SE:LP:SS:ID  0.051:0.067:0.346787:611.99:rs4970383
1   846808  rs4475691   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.037:0.032:0.60206:3060.98:rs4475691
1   846864  rs950122    G   C   .   PASS    .   ES:SE:LP:SS:ID  -0.016:0.13:0.0457575:611.24:rs950122
1   854250  rs7537756   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.13:0.075:1.05061:612:rs7537756
1   861808  rs13302982  A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.12:0.16:0.337242:612:rs13302982
1   863124  rs4040604   G   T   .   PASS    .   ES:SE:LP:SS:ID  -0.12:0.16:0.337242:612:rs4040604
1   870645  rs28576697  T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.045:0.066:0.309804:611.94:rs28576697
1   879317  rs7523549   C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.03:0.16:0.0705811:611.93:rs7523549
1   880238  rs3748592   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.039:0.13:0.119186:612:rs3748592
1   880390  rs3748593   C   A   .   PASS    .   ES:SE:LP:SS:ID  -0.023:0.18:0.0457575:612:rs3748593
1   882033  rs2272756   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.004:0.068:0.0222764:612:rs2272756
1   882803  rs2340582   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.027:0.13:0.0809219:611.99:rs2340582
1   884815  rs4246503   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.039:0.13:0.119186:612:rs4246503
1   886384  rs3748594   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.019:0.18:0.0362122:612:rs3748594
1   887560  rs3748595   A   C   .   PASS    .   ES:SE:LP:SS:ID  -0.07:0.12:0.251812:611.98:rs3748595
1   888659  rs3748597   T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.032:0.074:0.173925:1993:rs3748597
1   891945  rs13303106  A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.02:0.062:0.124939:611.99:rs13303106
1   894573  rs13303010  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.14:0.1:0.744727:611.99:rs13303010
1   900505  rs28705211  G   C   .   PASS    .   ES:SE:LP:SS:ID  0.0012:0.027:0.0177288:3061.73:rs28705211
1   900730  rs3935066   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.1:0.11:0.455932:612:rs3935066
1   903104  rs6696281   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.081:0.16:0.207608:612:rs6696281
1   908414  rs28504611  C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.035:0.18:0.0757207:611.95:rs28504611
1   916834  rs6694632   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.062:0.059:0.522879:612:rs6694632
1   918384  rs13303118  G   T   .   PASS    .   ES:SE:LP:SS:ID  -0.017:0.028:0.267606:2857.07:rs13303118
1   918573  rs2341354   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.05:0.034:0.853872:2004:rs2341354
1   924898  rs6665000   C   A   .   PASS    .   ES:SE:LP:SS:ID  0.031:0.18:0.0655015:612:rs6665000
1   926431  rs4970403   A   T   .   PASS    .   ES:SE:LP:SS:ID  -0.12:0.097:0.638272:1999:rs4970403