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}
*********************************************************************
* 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/folkersen-pqtl-gwas-import/processed/PROT-b-56/PROT-b-56.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/folkersen-pqtl-gwas-import/processed/PROT-b-56/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Mon Oct 28 22:10:17 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen-pqtl-gwas-import/processed/PROT-b-56/PROT-b-56.vcf.gz ...
Read summary statistics for 5135036 SNPs.
Dropped 1 SNPs with duplicated rs numbers.
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, 759193 SNPs remain.
After merging with regression SNP LD, 759193 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2798 (0.1798)
Lambda GC: 1.0018
Mean Chi^2: 1.0048
Intercept: 0.9828 (0.0099)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Oct 28 22:11:06 2019
Total time elapsed: 48.29s
{
"af_correlation": 0.9563,
"inflation_factor": 0.9907,
"mean_EFFECT": -0.0019,
"n": "-Inf",
"n_snps": 5135036,
"n_clumped_hits": 1,
"n_p_sig": 275,
"n_mono": 545,
"n_ns": 317497,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 377170,
"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": 759193,
"ldsc_nsnp_merge_regression_ld": 759193,
"ldsc_observed_scale_h2_beta": 0.2798,
"ldsc_observed_scale_h2_se": 0.1798,
"ldsc_intercept_beta": 0.9828,
"ldsc_intercept_se": 0.0099,
"ldsc_lambda_gc": 1.0018,
"ldsc_mean_chisq": 1.0048,
"ldsc_ratio": -3.5833
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | FALSE |
n | TRUE |
is_snpid_non_unique | TRUE |
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 | 5135032 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 3 | 0 | 80 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 3 | 0 | 80 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
logical | N | 5135036 | 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 | 8.356760e+00 | 5.629048e+00 | 1.0000 | 3.000000e+00 | 7.000000e+00 | 1.200000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.977423e+07 | 5.495317e+07 | 29422.0000 | 3.532730e+07 | 7.050636e+07 | 1.143548e+08 | 2.492183e+08 | ▇▇▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.910900e-03 | 2.954507e-01 | -10.3872 | -3.750000e-02 | -6.000000e-04 | 3.600000e-02 | 1.374100e+01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.338332e-01 | 2.420224e-01 | 0.0233 | 3.380000e-02 | 4.740000e-02 | 1.082000e-01 | 3.340500e+00 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.010800e-01 | 2.883211e-01 | 0.0000 | 2.518002e-01 | 5.020003e-01 | 7.505005e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.009170e-01 | 2.884220e-01 | 0.0000 | 2.514895e-01 | 5.018811e-01 | 7.504525e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.781589e-01 | 2.817943e-01 | 0.0000 | 3.560000e-02 | 1.762000e-01 | 4.617000e-01 | 1.000000e+00 | ▇▃▂▂▁ |
numeric | AF_reference | 377170 | 0.9265497 | NA | NA | NA | NA | NA | NA | NA | 2.522964e-01 | 2.538675e-01 | 0.0000 | 3.654150e-02 | 1.659350e-01 | 4.039540e-01 | 1.000000e+00 | ▇▃▂▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 780785 | rs2977612 | T | A | 0.0306 | 0.0464 | 0.5103005 | 0.5095858 | 0.8252 | 0.669329 | NA |
1 | 782981 | rs6594026 | C | T | -0.0301 | 0.0458 | 0.5109001 | 0.5110490 | 0.1534 | 0.297923 | NA |
1 | 783318 | rs6686696 | A | G | -0.0473 | 0.0717 | 0.5100996 | 0.5094508 | 0.0799 | 0.183107 | NA |
1 | 785050 | rs2905062 | G | A | 0.0224 | 0.0340 | 0.5104004 | 0.5100091 | 0.8365 | 0.626997 | NA |
1 | 785989 | rs2980300 | T | C | 0.0248 | 0.0377 | 0.5103005 | 0.5106506 | 0.8083 | 0.626997 | NA |
1 | 787121 | rs12077234 | T | A | -0.0392 | 0.0596 | 0.5106002 | 0.5107193 | 0.1319 | NA | NA |
1 | 787399 | rs2905055 | G | T | 0.0303 | 0.0461 | 0.5112002 | 0.5110094 | 0.8001 | 0.646366 | NA |
1 | 787685 | rs2905054 | G | T | 0.0291 | 0.0441 | 0.5103005 | 0.5093411 | 0.7668 | 0.622204 | NA |
1 | 787844 | rs2905053 | C | T | 0.0315 | 0.0479 | 0.5106002 | 0.5107823 | 0.8114 | 0.651757 | NA |
1 | 790758 | 1_790758_GTA_G | G | GTA | 0.0335 | 0.0510 | 0.5106002 | 0.5112692 | 0.7799 | NA | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51163039 | rs715584 | G | T | 0.0268 | 0.0301 | 0.3733997 | 0.3732697 | 0.4131 | 0.4736420 | NA |
22 | 51163138 | rs715586 | C | T | 0.0447 | 0.0361 | 0.2157998 | 0.2156318 | 0.1273 | 0.0902556 | NA |
22 | 51163910 | rs192700691 | C | T | 0.0914 | 0.1073 | 0.3945999 | 0.3943155 | 0.0304 | 0.0295527 | NA |
22 | 51164109 | rs5770995 | G | C | 0.0147 | 0.0283 | 0.6027997 | 0.6034577 | 0.4411 | 0.5109820 | NA |
22 | 51164115 | rs5770996 | C | T | 0.0147 | 0.0284 | 0.6065003 | 0.6047335 | 0.4446 | 0.5147760 | NA |
22 | 51164287 | rs6009957 | T | C | -0.0083 | 0.0273 | 0.7624002 | 0.7611056 | 0.3052 | 0.4155350 | NA |
22 | 51165664 | rs8137951 | G | A | -0.0084 | 0.0266 | 0.7507995 | 0.7521623 | 0.2954 | 0.4063500 | NA |
22 | 51171693 | rs756638 | G | A | -0.0323 | 0.0387 | 0.4041997 | 0.4039287 | 0.3046 | 0.3049120 | NA |
22 | 51175626 | rs3810648 | A | G | 0.0340 | 0.0603 | 0.5731998 | 0.5728580 | 0.0735 | 0.1084270 | NA |
22 | 51178090 | rs2285395 | G | A | 0.0319 | 0.0572 | 0.5770999 | 0.5770545 | 0.0481 | 0.0666933 | NA |
1 780785 rs2977612 T A . PASS AF=0.8252 ES:SE:LP:AF:ID 0.0306:0.0464:0.292174:0.8252:rs2977612
1 782981 rs6594026 C T . PASS AF=0.1534 ES:SE:LP:AF:ID -0.0301:0.0458:0.291664:0.1534:rs6594026
1 783318 rs6686696 A G . PASS AF=0.0799 ES:SE:LP:AF:ID -0.0473:0.0717:0.292345:0.0799:rs6686696
1 785050 rs2905062 G A . PASS AF=0.8365 ES:SE:LP:AF:ID 0.0224:0.034:0.292089:0.8365:rs2905062
1 785989 rs2980300 T C . PASS AF=0.8083 ES:SE:LP:AF:ID 0.0248:0.0377:0.292174:0.8083:rs2980300
1 787121 rs12077234 T A . PASS AF=0.1319 ES:SE:LP:AF:ID -0.0392:0.0596:0.291919:0.1319:rs12077234
1 787399 rs2905055 G T . PASS AF=0.8001 ES:SE:LP:AF:ID 0.0303:0.0461:0.291409:0.8001:rs2905055
1 787685 rs2905054 G T . PASS AF=0.7668 ES:SE:LP:AF:ID 0.0291:0.0441:0.292174:0.7668:rs2905054
1 787844 rs2905053 C T . PASS AF=0.8114 ES:SE:LP:AF:ID 0.0315:0.0479:0.291919:0.8114:rs2905053
1 790758 1_790758_GTA_G G GTA . PASS AF=0.7799 ES:SE:LP:AF:ID 0.0335:0.051:0.291919:0.7799:1_790758_GTA_G
1 1108637 rs4970421 G A . PASS AF=0.0713 ES:SE:LP:AF:ID -0.0591:0.0757:0.360812:0.0713:rs4970421
1 1112982 rs6671609 C T . PASS AF=0.1436 ES:SE:LP:AF:ID -0.0325:0.0601:0.230475:0.1436:rs6671609
1 1115994 rs13376597 G A . PASS AF=0.1429 ES:SE:LP:AF:ID -0.0322:0.0581:0.237396:0.1429:rs13376597
1 1116231 rs13374146 T C . PASS AF=0.0678 ES:SE:LP:AF:ID -0.0521:0.0612:0.403513:0.0678:rs13374146
1 1117398 rs12097586 A G . PASS AF=0.4246 ES:SE:LP:AF:ID 0.0318:0.0437:0.32994:0.4246:rs12097586
1 1117486 rs13376670 A G . PASS AF=0.1481 ES:SE:LP:AF:ID -0.0261:0.0571:0.188894:0.1481:rs13376670
1 1118275 rs61733845 C T . PASS AF=0.05 ES:SE:LP:AF:ID -0.0573:0.0576:0.494579:0.05:rs61733845
1 1118578 rs111290899 G A . PASS AF=0.0504 ES:SE:LP:AF:ID -0.0575:0.0589:0.483068:0.0504:rs111290899
1 1119657 rs4560982 G C . PASS AF=0.4012 ES:SE:LP:AF:ID 0.0353:0.0392:0.434388:0.4012:rs4560982
1 1119858 rs1320565 C T . PASS AF=0.1126 ES:SE:LP:AF:ID 0.0179:0.0603:0.115545:0.1126:rs1320565
1 1120431 rs1320571 G A . PASS AF=0.0525 ES:SE:LP:AF:ID 0.0356:0.0551:0.285251:0.0525:rs1320571
1 1121014 rs3813204 G A . PASS AF=0.1364 ES:SE:LP:AF:ID 0.0552:0.0571:0.476514:0.1364:rs3813204
1 1121341 rs4297230 C T . PASS AF=0.1422 ES:SE:LP:AF:ID 0.0598:0.0557:0.548982:0.1422:rs4297230
1 1121358 rs80057011 A C . PASS AF=0.0928 ES:SE:LP:AF:ID 0.0114:0.0656:0.064392:0.0928:rs80057011
1 1121480 rs12063663 T C . PASS AF=0.0923 ES:SE:LP:AF:ID -0.001:0.0654:0.00555086:0.0923:rs12063663
1 1121625 rs4081334 C G . PASS AF=0.1418 ES:SE:LP:AF:ID 0.0625:0.0552:0.58956:0.1418:rs4081334
1 1121657 rs11260548 T C . PASS AF=0.2302 ES:SE:LP:AF:ID 0.0284:0.0371:0.352911:0.2302:rs11260548
1 1121715 rs4081333 C T . PASS AF=0.0882 ES:SE:LP:AF:ID 0.0035:0.0644:0.0191334:0.0882:rs4081333
1 1121794 rs11260549 G A . PASS AF=0.1326 ES:SE:LP:AF:ID 0.0573:0.055:0.52739:0.1326:rs11260549
1 1121835 rs57346441 C CTG . PASS AF=0.2304 ES:SE:LP:AF:ID 0.0278:0.0363:0.352031:0.2304:1_1121835_C_CTG
1 1122024 rs4314833 T C . PASS AF=0.1279 ES:SE:LP:AF:ID 0.0534:0.0561:0.4675:0.1279:rs4314833
1 1122196 rs4634847 A G . PASS AF=0.1342 ES:SE:LP:AF:ID 0.0573:0.0547:0.530473:0.1342:rs4634847
1 1122283 rs12064046 T G . PASS AF=0.0862 ES:SE:LP:AF:ID 0.0042:0.0638:0.0231917:0.0862:rs12064046
1 1122319 rs7415847 C T . PASS AF=0.1199 ES:SE:LP:AF:ID 0.0587:0.0598:0.485851:0.1199:rs7415847
1 1122468 rs7545694 T C . PASS AF=0.2031 ES:SE:LP:AF:ID 0.0249:0.04:0.272621:0.2031:rs7545694
1 1122516 rs11260551 G A . PASS AF=0.1274 ES:SE:LP:AF:ID 0.0502:0.0559:0.432974:0.1274:rs11260551
1 1122539 rs12063897 A G . PASS AF=0.0866 ES:SE:LP:AF:ID 0.0048:0.0631:0.0270108:0.0866:rs12063897
1 1122915 rs28595293 A G . PASS AF=0.2718 ES:SE:LP:AF:ID 0.0313:0.032:0.483729:0.2718:rs28595293
1 1122916 rs28460227 A G . PASS AF=0.0856 ES:SE:LP:AF:ID 0.004:0.0632:0.0224136:0.0856:rs28460227
1 1122937 rs28648687 G A . PASS AF=0.0856 ES:SE:LP:AF:ID 0.004:0.0631:0.022505:0.0856:rs28648687
1 1123106 rs12401472 G A . PASS AF=0.128 ES:SE:LP:AF:ID 0.0497:0.0554:0.431564:0.128:rs12401472
1 1123434 rs12066716 T A . PASS AF=0.1323 ES:SE:LP:AF:ID 0.0313:0.0537:0.25189:0.1323:rs12066716
1 1124257 rs10907172 A G . PASS AF=0.1273 ES:SE:LP:AF:ID 0.0494:0.0552:0.431095:0.1273:rs10907172
1 1124399 rs10907173 C G . PASS AF=0.1324 ES:SE:LP:AF:ID 0.0524:0.054:0.479516:0.1324:rs10907173
1 1124663 rs6684820 G A . PASS AF=0.2737 ES:SE:LP:AF:ID 0.0306:0.0313:0.484656:0.2737:rs6684820
1 1124819 rs6694487 C T . PASS AF=0.0867 ES:SE:LP:AF:ID 0.0056:0.0625:0.0323116:0.0867:rs6694487
1 1124891 rs61768485 G A . PASS AF=0.1266 ES:SE:LP:AF:ID 0.0492:0.055:0.430392:0.1266:rs61768485
1 1125110 rs12124436 T C . PASS AF=0.1248 ES:SE:LP:AF:ID 0.049:0.0548:0.430509:0.1248:rs12124436
1 1125220 rs12065129 C T . PASS AF=0.0864 ES:SE:LP:AF:ID 0.006:0.0619:0.0347042:0.0864:rs12065129
1 1125348 rs12029885 T C . PASS AF=0.1261 ES:SE:LP:AF:ID 0.0526:0.0552:0.467883:0.1261:rs12029885