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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_20001_1022.vcf.gz --id UKB-b:20145 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20001_1022.txt.gz --cohort_cases 1494 --cohort_controls 461439 --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": "2019-09-13T07:56:21.025630",
"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-20145/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20145/UKB-b-20145_raw.vcf.gz; Date=Thu Oct 17 12:38:52 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-20145/ukb-b-20145.vcf.gz; Date=Sun May 10 08:20:31 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-20145/UKB-b-20145_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20145/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:06 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20145/UKB-b-20145_data.vcf.gz ...
Read summary statistics for 2489144 SNPs.
Dropped 291 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, 630119 SNPs remain.
After merging with regression SNP LD, 630119 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0013 (0.0012)
Lambda GC: 1.0233
Mean Chi^2: 1.0175
Intercept: 1.0031 (0.0095)
Ratio: 0.1796 (0.5423)
Analysis finished at Thu Oct 17 14:42:43 2019
Total time elapsed: 37.33s
{
"af_correlation": 0.7672,
"inflation_factor": 1,
"mean_EFFECT": 7.2099e-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": 19742,
"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": 630119,
"ldsc_nsnp_merge_regression_ld": 630119,
"ldsc_observed_scale_h2_beta": 0.0013,
"ldsc_observed_scale_h2_se": 0.0012,
"ldsc_intercept_beta": 1.0031,
"ldsc_intercept_se": 0.0095,
"ldsc_lambda_gc": 1.0233,
"ldsc_mean_chisq": 1.0175,
"ldsc_ratio": 0.1771
}
name | value |
---|---|
af_correlation | FALSE |
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 | 2488856 | 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 | 2489144 | 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 | 8.652492e+00 | 5.766030e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.855676e+07 | 5.662451e+07 | 5687.0000000 | 3.168024e+07 | 6.898619e+07 | 1.147558e+08 | 2.491917e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.000000e-07 | 1.265000e-04 | -0.0006292 | -8.440000e-05 | 8.000000e-07 | 8.560000e-05 | 7.039000e-04 | ▁▂▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.253000e-04 | 6.700000e-06 | 0.0001138 | 1.196000e-04 | 1.234000e-04 | 1.299000e-04 | 2.463000e-04 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.976535e-01 | 2.899465e-01 | 0.0000001 | 2.500000e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.976561e-01 | 2.899206e-01 | 0.0000001 | 2.453053e-01 | 4.963522e-01 | 7.494949e-01 | 9.999994e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.537708e-01 | 1.511054e-01 | 0.2342710 | 3.209720e-01 | 4.315490e-01 | 5.750650e-01 | 7.657290e-01 | ▇▆▅▅▃ |
numeric | AF_reference | 19742 | 0.9920688 | NA | NA | NA | NA | NA | NA | NA | 4.353417e-01 | 1.761076e-01 | 0.0001997 | 2.963260e-01 | 4.199280e-01 | 5.640970e-01 | 1.000000e+00 | ▂▇▇▃▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 49298 | rs200943160 | T | C | -0.0004077 | 0.0002093 | 0.0510000 | 0.0514825 | 0.623763 | 0.7821490 | NA |
1 | 54676 | rs2462492 | C | T | 0.0001776 | 0.0002074 | 0.3900004 | 0.3919371 | 0.400401 | NA | NA |
1 | 91536 | rs6702460 | G | T | -0.0000802 | 0.0002042 | 0.6899999 | 0.6945678 | 0.456851 | 0.4207270 | NA |
1 | 534192 | rs6680723 | C | T | 0.0002568 | 0.0002333 | 0.2700001 | 0.2708721 | 0.240960 | NA | NA |
1 | 706368 | rs55727773 | A | G | -0.0000485 | 0.0001448 | 0.7400005 | 0.7377132 | 0.515650 | 0.2751600 | NA |
1 | 763394 | rs369924889 | G | A | -0.0003207 | 0.0001698 | 0.0589997 | 0.0588846 | 0.706753 | 0.6176120 | NA |
1 | 768253 | rs2977608 | A | C | -0.0000723 | 0.0001386 | 0.5999997 | 0.6016182 | 0.761304 | 0.4894170 | NA |
1 | 776546 | rs12124819 | A | G | -0.0000672 | 0.0001548 | 0.6600001 | 0.6642158 | 0.265390 | 0.0756789 | NA |
1 | 814495 | rs74461805 | C | A | -0.0001863 | 0.0001986 | 0.3500000 | 0.3482048 | 0.340397 | NA | NA |
1 | 830181 | rs28444699 | A | G | -0.0001152 | 0.0001328 | 0.3900004 | 0.3856267 | 0.697259 | 0.6912940 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51180501 | rs5770999 | T | C | 0.0000720 | 0.0001363 | 0.5999997 | 0.5971453 | 0.713658 | 0.6369810 | NA |
22 | 51181919 | rs9616825 | G | C | 0.0001566 | 0.0001356 | 0.2500000 | 0.2482073 | 0.695471 | 0.6194090 | NA |
22 | 51182485 | rs6009961 | A | G | 0.0000927 | 0.0001367 | 0.5000000 | 0.4977210 | 0.715505 | 0.6383790 | NA |
22 | 51186143 | rs2879914 | T | C | -0.0001231 | 0.0001268 | 0.3300000 | 0.3317003 | 0.381826 | 0.2733630 | NA |
22 | 51186228 | rs3865766 | C | T | -0.0000465 | 0.0001236 | 0.7099994 | 0.7068202 | 0.451063 | 0.4532750 | NA |
22 | 51197266 | rs61290853 | A | G | 0.0000011 | 0.0001276 | 0.9900000 | 0.9930588 | 0.386333 | 0.4229230 | NA |
22 | 51198027 | rs34939255 | A | G | 0.0001137 | 0.0001444 | 0.4299995 | 0.4311395 | 0.254557 | 0.0984425 | NA |
22 | 51211106 | rs9628250 | T | C | 0.0001147 | 0.0001432 | 0.4199997 | 0.4231873 | 0.271547 | 0.1671330 | NA |
22 | 51212875 | rs2238837 | A | C | -0.0002379 | 0.0001360 | 0.0800000 | 0.0803939 | 0.331455 | 0.3724040 | NA |
22 | 51237063 | rs3896457 | T | C | -0.0000843 | 0.0001393 | 0.5400003 | 0.5448451 | 0.297971 | 0.2050720 | NA |
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