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"gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_41229_5K8.vcf.gz --id UKB-b:5644 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41229_5K8.txt.gz --cohort_cases 1011 --cohort_controls 461999 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
"file_date": "2019-09-13T07:01:51.357927",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -T ^/mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5644/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5644/UKB-b-5644_raw.vcf.gz; Date=Thu Oct 17 12:45:13 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-5644/ukb-b-5644.vcf.gz; Date=Sat May 9 14:59:42 2020"
}
*********************************************************************
* 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/public/UKB-b-5644/UKB-b-5644_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5644/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:45:32 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5644/UKB-b-5644_data.vcf.gz ...
Read summary statistics for 1370023 SNPs.
Dropped 112 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 354867 SNPs remain.
After merging with regression SNP LD, 354867 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0061 (0.0018)
Lambda GC: 1.0698
Mean Chi^2: 1.0794
Intercept: 1.0104 (0.0126)
Ratio: 0.131 (0.1592)
Analysis finished at Thu Oct 17 14:45:56 2019
Total time elapsed: 24.22s
{
"af_correlation": 0.5584,
"inflation_factor": 1.0475,
"mean_EFFECT": -4.7211e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 0,
"n_p_sig": 0,
"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": 0,
"n_miss_AF_reference": 10938,
"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": 354867,
"ldsc_nsnp_merge_regression_ld": 354867,
"ldsc_observed_scale_h2_beta": 0.0061,
"ldsc_observed_scale_h2_se": 0.0018,
"ldsc_intercept_beta": 1.0104,
"ldsc_intercept_se": 0.0126,
"ldsc_lambda_gc": 1.0698,
"ldsc_mean_chisq": 1.0794,
"ldsc_ratio": 0.131
}
name | value |
---|---|
af_correlation | TRUE |
inflation_factor | FALSE |
n | TRUE |
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 |
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 SNPsn_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:
A, C, G or T
.< 0
or > 1
.<= 0
or = Infinity
).< 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.
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.
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.
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.
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
> 0.5ldsc_intercept_beta
: ldsc_intercept_beta
> 1.5n_clumped_hits
: n_clumped_hits
> 1000r2_sum<*>
: r2_sum<*>
> 0.5Plots
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 | 0 | 1.0000000 | 4 | 58 | 0 | 1369913 | 0 | NA | NA | 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 | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
logical | N | 1370023 | 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 | 8.681283e+00 | 5.768365e+00 | 1.00000e+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 | 7.847044e+07 | 5.650797e+07 | 1.23330e+04 | 3.162723e+07 | 6.894256e+07 | 1.143796e+08 | 2.491722e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -5.000000e-07 | 1.028000e-04 | -4.64800e-04 | -6.930000e-05 | 0.000000e+00 | 6.870000e-05 | 5.518000e-04 | ▁▃▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 9.910000e-05 | 2.500000e-06 | 9.36000e-05 | 9.760000e-05 | 9.860000e-05 | 1.001000e-04 | 1.850000e-04 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.891902e-01 | 2.922925e-01 | 8.00000e-07 | 2.300001e-01 | 4.899999e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.891921e-01 | 2.922683e-01 | 8.00000e-07 | 2.328476e-01 | 4.857515e-01 | 7.434895e-01 | 9.999965e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.847793e-01 | 8.846410e-02 | 3.46192e-01 | 4.069080e-01 | 4.771060e-01 | 5.583715e-01 | 6.538080e-01 | ▇▇▆▆▅ |
numeric | AF_reference | 10938 | 0.9920162 | NA | NA | NA | NA | NA | NA | NA | 4.624996e-01 | 1.417192e-01 | 1.99700e-04 | 3.572280e-01 | 4.570690e-01 | 5.634980e-01 | 1.000000e+00 | ▁▆▇▃▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 49298 | rs200943160 | T | C | 0.0000175 | 0.0001722 | 0.9199999 | 0.9190531 | 0.623765 | 0.782149 | NA |
1 | 54676 | rs2462492 | C | T | 0.0000881 | 0.0001706 | 0.6100002 | 0.6054039 | 0.400401 | NA | NA |
1 | 91536 | rs6702460 | G | T | 0.0003554 | 0.0001680 | 0.0340001 | 0.0343554 | 0.456846 | 0.420727 | NA |
1 | 706368 | rs55727773 | A | G | -0.0000033 | 0.0001191 | 0.9800000 | 0.9778342 | 0.515645 | 0.275160 | NA |
1 | 840753 | rs4970382 | T | C | 0.0001613 | 0.0000990 | 0.1000000 | 0.1031966 | 0.400124 | 0.468850 | NA |
1 | 843405 | rs11516185 | A | G | 0.0000086 | 0.0001229 | 0.9400001 | 0.9441541 | 0.362606 | 0.375399 | NA |
1 | 850218 | rs6664536 | T | A | -0.0000535 | 0.0000987 | 0.5900000 | 0.5878597 | 0.590331 | 0.345248 | NA |
1 | 850371 | rs6679046 | G | T | -0.0001082 | 0.0000992 | 0.2800000 | 0.2755853 | 0.603723 | 0.508786 | NA |
1 | 850780 | rs6657440 | C | T | -0.0001041 | 0.0000992 | 0.2900000 | 0.2941281 | 0.603942 | 0.560304 | NA |
1 | 852037 | rs4970463 | G | A | -0.0000554 | 0.0000988 | 0.5700002 | 0.5748595 | 0.589686 | 0.345048 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51158017 | rs6010065 | G | C | 6.41e-05 | 0.0000973 | 0.5099998 | 0.5097317 | 0.461411 | 0.547524 | NA |
22 | 51158499 | rs8136930 | T | G | 5.50e-05 | 0.0000974 | 0.5700002 | 0.5725414 | 0.461636 | 0.544728 | NA |
22 | 51161019 | rs5770994 | C | T | -7.01e-05 | 0.0000971 | 0.4700002 | 0.4703297 | 0.482204 | 0.425719 | NA |
22 | 51163039 | rs715584 | G | T | 5.71e-05 | 0.0000986 | 0.5600000 | 0.5625466 | 0.426975 | 0.473642 | NA |
22 | 51164109 | rs5770995 | G | C | 4.73e-05 | 0.0000980 | 0.6300007 | 0.6293541 | 0.452705 | 0.510982 | NA |
22 | 51164115 | rs5770996 | C | T | 3.92e-05 | 0.0000979 | 0.6899999 | 0.6888769 | 0.456917 | 0.514776 | NA |
22 | 51174048 | rs9628245 | G | C | 5.51e-05 | 0.0001106 | 0.6200004 | 0.6183224 | 0.380135 | 0.433107 | NA |
22 | 51186143 | rs2879914 | T | C | 3.45e-05 | 0.0001043 | 0.7400005 | 0.7406914 | 0.381825 | 0.273363 | NA |
22 | 51186228 | rs3865766 | C | T | -1.35e-05 | 0.0001016 | 0.8900000 | 0.8946480 | 0.451061 | 0.453275 | NA |
22 | 51197266 | rs61290853 | A | G | -1.73e-05 | 0.0001049 | 0.8700001 | 0.8693901 | 0.386333 | 0.422923 | NA |
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