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-109/ieu-a-109.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-109/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Wed Feb  5 11:20:11 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-109/ieu-a-109.vcf.gz ...
Read summary statistics for 2736763 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, 1271845 SNPs remain.
After merging with regression SNP LD, 1271845 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1047 (0.0121)
Lambda GC: 1.0047
Mean Chi^2: 1.02
Intercept: 0.9438 (0.0047)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 11:20:43 2020
Total time elapsed: 32.21s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9172,
    "inflation_factor": 1,
    "mean_EFFECT": 0.0005,
    "n": 42733.9,
    "n_snps": 2736763,
    "n_clumped_hits": 6,
    "n_p_sig": 224,
    "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": 477203,
    "n_miss_AF_reference": 26840,
    "n_est": 42731.9129,
    "ratio_se_n": 1,
    "mean_diff": -0,
    "ratio_diff": 1.4994,
    "sd_y_est1": 1.0447,
    "sd_y_est2": 1.0447,
    "r2_sum1": 0.0047,
    "r2_sum2": 0.0043,
    "r2_sum3": 0.0043,
    "r2_sum4": 0.0045,
    "ldsc_nsnp_merge_refpanel_ld": 1271845,
    "ldsc_nsnp_merge_regression_ld": 1271845,
    "ldsc_observed_scale_h2_beta": 0.1047,
    "ldsc_observed_scale_h2_se": 0.0121,
    "ldsc_intercept_beta": 0.9438,
    "ldsc_intercept_se": 0.0047,
    "ldsc_lambda_gc": 1.0047,
    "ldsc_mean_chisq": 1.02,
    "ldsc_ratio": -2.81
}

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 2736763 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 8.614067e+00 5.688409e+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 7.881436e+07 5.590196e+07 6689.0000 3.245412e+07 7.000232e+07 1.144374e+08 2.492114e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 5.414000e-04 2.822045e-01 -160.0000 -7.300000e-03 0.000000e+00 7.400000e-03 1.900000e+02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.434330e-02 9.925817e-01 0.0068 7.700000e-03 9.400000e-03 1.500000e-02 6.000000e+02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.992586e-01 2.892623e-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 4.994560e-01 2.891608e-01 0.0000 2.485632e-01 4.996758e-01 7.496904e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 477203 0.8256323 NA NA NA NA NA 3.565770e-01 2.754927e-01 0.0083 1.167000e-01 2.917000e-01 5.583000e-01 9.917000e-01 ▇▅▃▂▂
numeric AF_reference 26840 0.9901928 NA NA NA NA NA 3.543236e-01 2.612930e-01 0.0000 1.341850e-01 2.887380e-01 5.409350e-01 1.000000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 3.802059e+04 1.128623e+04 120.0000 4.078740e+04 4.272690e+04 4.273140e+04 4.273390e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 564477 rs6650104 A G -0.1400 0.230 0.5500004 0.5427262 NA 0.0003994 345.85
1 567753 rs532073948 A G -0.1400 0.230 0.5300002 0.5427262 NA 0.0005990 2070.00
1 721290 rs12565286 G C -0.0083 0.029 0.7800007 0.7747197 NA 0.0371406 19827.00
1 723819 rs11804171 T A -0.0110 0.029 0.7099994 0.7044574 NA 0.1345850 19845.00
1 723891 rs2977670 G C -0.0230 0.042 0.5900000 0.5839535 NA 0.7799520 8718.97
1 752566 rs3094315 G A 0.0070 0.012 0.5600000 0.5596689 NA 0.7182510 28467.80
1 752721 rs3131972 A G 0.0890 0.100 0.3700002 0.3734659 NA 0.6533550 345.93
1 753541 rs2073813 G A -0.0120 0.016 0.4600002 0.4532547 NA 0.3019170 20094.00
1 754182 rs3131969 A G 0.0770 0.100 0.4600002 0.4412999 NA 0.6785140 345.99
1 754192 rs3131968 A G -0.0130 0.022 0.5600000 0.5545813 NA 0.6785140 10730.40
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51211392 rs3888396 T C -0.1000 0.0420 0.0129999 0.0172679 NA 0.1641370 11263.0
22 51212875 rs2238837 A C 0.0300 0.0120 0.0150000 0.0124193 0.3917 0.3724040 25263.3
22 51213613 rs34726907 C T 0.0350 0.0460 0.4400003 0.4467350 NA 0.1727240 1889.0
22 51219006 rs28729663 G A 0.0058 0.0410 0.8900000 0.8875039 NA 0.2052720 2052.0
22 51229805 rs9616985 T C 0.0660 0.0250 0.0083000 0.0082906 0.0917 0.0730831 21965.9
23 35921591 rs2204667 C G -0.0067 0.0096 0.4899999 0.4852293 0.1667 NA 42728.4
23 51666786 rs14115 A G 0.0005 0.0160 0.9699999 0.9750702 0.0250 NA 42641.1
23 70163799 rs1626496 A C -0.0007 0.0140 0.9599999 0.9601224 0.0750 NA 42612.9
23 91415872 rs6562597 G A -0.0240 0.0260 0.3599996 0.3559671 0.0083 0.0021192 40442.3
23 118495837 rs12882977 G A -0.0065 0.0071 0.3599996 0.3599329 0.5167 0.2307280 42730.3

bcf preview

1   564477  rs6650104   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.14:0.23:0.259637:345.85:rs6650104
1   567753  rs11510103  A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.14:0.23:0.275724:2070:rs11510103
1   721290  rs12565286  G   C   .   PASS    .   ES:SE:LP:SS:ID  -0.0083:0.029:0.107905:19827:rs12565286
1   723819  rs11804171  T   A   .   PASS    .   ES:SE:LP:SS:ID  -0.011:0.029:0.148742:19845:rs11804171
1   723891  rs2977670   G   C   .   PASS    .   ES:SE:LP:SS:ID  -0.023:0.042:0.229148:8718.97:rs2977670
1   752566  rs3094315   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.007:0.012:0.251812:28467.8:rs3094315
1   752721  rs3131972   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.089:0.1:0.431798:345.93:rs3131972
1   753541  rs2073813   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.012:0.016:0.337242:20094:rs2073813
1   754182  rs3131969   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.077:0.1:0.337242:345.99:rs3131969
1   754192  rs3131968   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.013:0.022:0.251812:10730.4:rs3131968
1   760912  rs1048488   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.09:0.1:0.431798:346:rs1048488
1   761732  rs2286139   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.034:0.039:0.408935:2043:rs2286139
1   768448  rs12562034  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.041:0.023:1.10237:16197.4:rs12562034
1   775659  rs2905035   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0034:0.013:0.09691:30823.7:rs2905035
1   776546  rs12124819  A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.0093:0.024:0.154902:5507.12:rs12124819
1   777122  rs2980319   A   T   .   PASS    .   ES:SE:LP:SS:ID  0.0039:0.013:0.113509:30824.7:rs2980319
1   779322  rs4040617   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.004:0.013:0.119186:30781.8:rs4040617
1   780785  rs2977612   T   A   .   PASS    .   ES:SE:LP:SS:ID  0.0037:0.013:0.107905:30823.7:rs2977612
1   784023  rs17160939  A   G   .   PASS    .   ES:SE:LP:SS:ID  0.072:0.12:0.275724:2591.97:rs17160939
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0036:0.013:0.102373:30823.7:rs2905062
1   785989  rs2980300   T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0025:0.013:0.0705811:30752.7:rs2980300
1   798026  rs4951864   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.026:0.023:0.60206:17303.4:rs4951864
1   798801  rs12132517  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.028:0.023:0.657577:17303.1:rs12132517
1   798959  rs11240777  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0045:0.015:0.119186:19240.2:rs11240777
1   838555  rs4970383   C   A   .   PASS    .   ES:SE:LP:SS:ID  -0.081:0.093:0.420216:346:rs4970383
1   846808  rs4475691   C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.017:0.036:0.200659:2819.97:rs4475691
1   846864  rs950122    G   C   .   PASS    .   ES:SE:LP:SS:ID  -0.28:0.17:0.958607:345.44:rs950122
1   854250  rs7537756   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.045:0.1:0.180456:346:rs7537756
1   861808  rs13302982  A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.2:0.21:0.49485:346:rs13302982
1   863124  rs4040604   G   T   .   PASS    .   ES:SE:LP:SS:ID  -0.2:0.21:0.49485:346:rs4040604
1   870645  rs28576697  T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.19:0.088:1.52288:345.96:rs28576697
1   879317  rs7523549   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.25:0.23:0.552842:345.98:rs7523549
1   880238  rs3748592   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.069:0.18:0.154902:346:rs3748592
1   880390  rs3748593   C   A   .   PASS    .   ES:SE:LP:SS:ID  0.1:0.25:0.173925:346:rs3748593
1   882033  rs2272756   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.037:0.058:0.283997:1978:rs2272756
1   882803  rs2340582   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.069:0.18:0.154902:346:rs2340582
1   884815  rs4246503   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.069:0.18:0.154902:346:rs4246503
1   886384  rs3748594   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.15:0.23:0.309804:346:rs3748594
1   887560  rs3748595   A   C   .   PASS    .   ES:SE:LP:SS:ID  -0.1:0.17:0.275724:346:rs3748595
1   888659  rs3748597   T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.053:0.058:0.443698:2287:rs3748597
1   891945  rs13303106  A   G   .   PASS    .   ES:SE:LP:SS:ID  0.045:0.081:0.244125:346:rs13303106
1   894573  rs13303010  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.21:0.14:0.886057:346:rs13303010
1   900505  rs28705211  G   C   .   PASS    .   ES:SE:LP:SS:ID  0.02:0.031:0.275724:2819.82:rs28705211
1   900730  rs3935066   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.24:0.15:0.958607:346:rs3935066
1   903104  rs6696281   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.16:0.22:0.318759:346:rs6696281
1   908414  rs28504611  C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.055:0.25:0.0809219:345.97:rs28504611
1   916834  rs6694632   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.027:0.078:0.142668:346:rs6694632
1   918384  rs13303118  G   T   .   PASS    .   ES:SE:LP:SS:ID  -0.024:0.029:0.376751:2591.12:rs13303118
1   918573  rs2341354   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.029:0.03:0.468521:2072:rs2341354
1   924898  rs6665000   C   A   .   PASS    .   ES:SE:LP:SS:ID  -0.14:0.24:0.259637:346:rs6665000