manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
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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_6154_6.vcf.gz --id UKB-b:11461 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_6154_6.txt.gz --cohort_cases 13478 --cohort_controls 444069 --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": "2019-09-13T01:55:03.024321",
"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-11461/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11461/UKB-b-11461_raw.vcf.gz; Date=Thu Oct 17 12:25:27 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-11461/ukb-b-11461.vcf.gz; Date=Sun May 10 11:05:03 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-11461/UKB-b-11461_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11461/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11461/UKB-b-11461_data.vcf.gz ...
Read summary statistics for 6374490 SNPs.
Dropped 3320 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, 1237046 SNPs remain.
After merging with regression SNP LD, 1237046 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0133 (0.0014)
Lambda GC: 1.1243
Mean Chi^2: 1.1345
Intercept: 1.013 (0.0072)
Ratio: 0.0963 (0.0536)
Analysis finished at Thu Oct 17 14:41:34 2019
Total time elapsed: 1.0m:15.34s
{
"af_correlation": 0.9294,
"inflation_factor": 1.0966,
"mean_EFFECT": -6.2676e-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": 58405,
"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": 1237046,
"ldsc_nsnp_merge_regression_ld": 1237046,
"ldsc_observed_scale_h2_beta": 0.0133,
"ldsc_observed_scale_h2_se": 0.0014,
"ldsc_intercept_beta": 1.013,
"ldsc_intercept_se": 0.0072,
"ldsc_lambda_gc": 1.1243,
"ldsc_mean_chisq": 1.1345,
"ldsc_ratio": 0.0967
}
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 | 3 | 58 | 0 | 6371191 | 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 | 6374490 | 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 | 8.666998e+00 | 5.763552e+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 | 7.857578e+07 | 5.649755e+07 | 828.0000000 | 3.201484e+07 | 6.900923e+07 | 1.144907e+08 | 2.492385e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -6.000000e-07 | 6.176000e-04 | -0.0047743 | -3.597000e-04 | -1.900000e-06 | 3.555000e-04 | 5.641800e-03 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.501000e-04 | 2.106000e-04 | 0.0003399 | 3.785000e-04 | 4.656000e-04 | 6.705000e-04 | 2.945500e-03 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.818591e-01 | 2.936063e-01 | 0.0000001 | 2.200002e-01 | 4.799997e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▆▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.818607e-01 | 2.935805e-01 | 0.0000001 | 2.232855e-01 | 4.757931e-01 | 7.360832e-01 | 9.999995e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.976644e-01 | 2.565493e-01 | 0.0259690 | 8.135200e-02 | 2.101440e-01 | 4.603050e-01 | 9.740300e-01 | ▇▃▂▂▁ |
numeric | AF_reference | 58405 | 0.9908377 | NA | NA | NA | NA | NA | NA | NA | 2.949504e-01 | 2.491061e-01 | 0.0000000 | 9.065500e-02 | 2.192490e-01 | 4.520770e-01 | 1.000000e+00 | ▇▅▂▂▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 49298 | rs200943160 | T | C | -0.0002718 | 0.0006256 | 0.6600001 | 0.6639867 | 0.623783 | 0.7821490 | NA |
1 | 54676 | rs2462492 | C | T | -0.0007344 | 0.0006197 | 0.2399999 | 0.2359977 | 0.400457 | NA | NA |
1 | 86028 | rs114608975 | T | C | -0.0002614 | 0.0009909 | 0.7899998 | 0.7919502 | 0.103543 | 0.0277556 | NA |
1 | 91536 | rs6702460 | G | T | 0.0003425 | 0.0006101 | 0.5700002 | 0.5746130 | 0.456874 | 0.4207270 | NA |
1 | 234313 | rs8179466 | C | T | 0.0003793 | 0.0012029 | 0.7499995 | 0.7524995 | 0.074519 | NA | NA |
1 | 534192 | rs6680723 | C | T | 0.0009473 | 0.0006969 | 0.1700000 | 0.1740564 | 0.240975 | NA | NA |
1 | 546697 | rs12025928 | A | G | -0.0008318 | 0.0008693 | 0.3400001 | 0.3386685 | 0.913488 | NA | NA |
1 | 693731 | rs12238997 | A | G | -0.0002752 | 0.0005839 | 0.6400000 | 0.6373509 | 0.116354 | 0.1417730 | NA |
1 | 705882 | rs72631875 | G | A | 0.0002554 | 0.0008557 | 0.7700005 | 0.7653831 | 0.067296 | 0.0315495 | NA |
1 | 706368 | rs55727773 | A | G | 0.0003401 | 0.0004327 | 0.4299995 | 0.4318258 | 0.515658 | 0.2751600 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51218377 | rs2519461 | G | C | -0.0002454 | 0.0006762 | 0.7199992 | 0.7166161 | 0.073602 | 0.0826677 | NA |
22 | 51219006 | rs28729663 | G | A | -0.0000842 | 0.0005220 | 0.8700001 | 0.8717829 | 0.137921 | 0.2052720 | NA |
22 | 51219387 | rs9616832 | T | C | -0.0002093 | 0.0006776 | 0.7600007 | 0.7573478 | 0.073721 | 0.0654952 | NA |
22 | 51219704 | rs147475742 | G | A | -0.0005966 | 0.0009079 | 0.5099998 | 0.5111348 | 0.041945 | 0.0473243 | NA |
22 | 51221190 | rs369304721 | G | A | -0.0003241 | 0.0009063 | 0.7199992 | 0.7206646 | 0.049724 | NA | NA |
22 | 51221731 | rs115055839 | T | C | -0.0002787 | 0.0006780 | 0.6800001 | 0.6810743 | 0.073211 | 0.0625000 | NA |
22 | 51222100 | rs114553188 | G | T | 0.0002809 | 0.0007982 | 0.7199992 | 0.7248579 | 0.054450 | 0.0880591 | NA |
22 | 51223637 | rs375798137 | G | A | 0.0002843 | 0.0008021 | 0.7199992 | 0.7229504 | 0.054078 | 0.0788738 | NA |
22 | 51229805 | rs9616985 | T | C | -0.0002684 | 0.0006804 | 0.6899999 | 0.6932180 | 0.073046 | 0.0730831 | NA |
22 | 51237063 | rs3896457 | T | C | 0.0005942 | 0.0004161 | 0.1499999 | 0.1532633 | 0.297942 | 0.2050720 | NA |
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