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"Gwas2VCF_command": "--data /data/cromwell-executions/qc/42a46ee9-c6e8-4176-b1ee-be8b00631f90/call-vcf/inputs/-261044534/upload.txt.gz --id ieu-b-4819 --json /data/cromwell-executions/qc/42a46ee9-c6e8-4176-b1ee-be8b00631f90/call-vcf/inputs/-261044534/ieu-b-4819_data.json --ref /data/cromwell-executions/qc/42a46ee9-c6e8-4176-b1ee-be8b00631f90/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/42a46ee9-c6e8-4176-b1ee-be8b00631f90/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-4819/ieu-b-4819.vcf.gz --alias alias.txt; 1.3.0",
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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 /data/cromwell-executions/qc/42a46ee9-c6e8-4176-b1ee-be8b00631f90/call-ldsc/inputs/-261044534/ieu-b-4819.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4819/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Wed Jan 5 04:39:20 2022
Reading summary statistics from /data/cromwell-executions/qc/42a46ee9-c6e8-4176-b1ee-be8b00631f90/call-ldsc/inputs/-261044534/ieu-b-4819.vcf.gz ...
Read summary statistics for 6046988 SNPs.
Dropped 16724 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1152796 SNPs remain.
After merging with regression SNP LD, 1152796 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0093 (0.0359)
Lambda GC: 1.0189
Mean Chi^2: 1.0244
Intercept: 1.0219 (0.0066)
Ratio: 0.8968 (0.2693)
Analysis finished at Wed Jan 5 04:40:46 2022
Total time elapsed: 1.0m:25.64s
{
"af_correlation": "NA",
"inflation_factor": 1.0226,
"mean_EFFECT": 0.0003,
"n": 12542,
"n_snps": 6047010,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 0,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 6047010,
"n_miss_AF_reference": 39453,
"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": 1152796,
"ldsc_nsnp_merge_regression_ld": 1152796,
"ldsc_observed_scale_h2_beta": 0.0093,
"ldsc_observed_scale_h2_se": 0.0359,
"ldsc_intercept_beta": 1.0219,
"ldsc_intercept_se": 0.0066,
"ldsc_lambda_gc": 1.0189,
"ldsc_mean_chisq": 1.0244,
"ldsc_ratio": 0.8975
}
name | value |
---|---|
af_correlation | NA |
inflation_factor | FALSE |
n | FALSE |
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 | TRUE |
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 | 6 | 0.9999990 | 3 | 58 | 0 | 6046991 | 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 | AF | 6047010 | 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 | 8.630937e+00 | 5.740717e+00 | 1.000e+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 | 7.888937e+07 | 5.640061e+07 | 8.280e+02 | 3.241012e+07 | 6.951510e+07 | 1.147393e+08 | 2.492223e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.697000e-04 | 8.895520e-02 | -7.505e-01 | -5.000000e-02 | 4.000000e-04 | 5.040000e-02 | 7.880000e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 8.129460e-02 | 3.230720e-02 | 4.450e-02 | 5.670000e-02 | 6.800000e-02 | 9.580000e-02 | 2.270000e-01 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.960387e-01 | 2.900105e-01 | 1.000e-07 | 2.435000e-01 | 4.952004e-01 | 7.473998e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.960388e-01 | 2.900110e-01 | 1.000e-07 | 2.435256e-01 | 4.951945e-01 | 7.473981e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF_reference | 39453 | 0.9934756 | NA | NA | NA | NA | NA | NA | NA | 3.043527e-01 | 2.467845e-01 | 1.997e-04 | 1.018370e-01 | 2.318290e-01 | 4.628590e-01 | 1.000000e+00 | ▇▅▂▂▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.163247e+04 | 1.108893e+03 | 7.088e+03 | 1.138900e+04 | 1.189700e+04 | 1.254200e+04 | 1.254200e+04 | ▁▁▁▁▇ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 797440 | rs58013264 | T | C | -0.1021 | 0.0925 | 0.2699001 | 0.2696869 | NA | 0.189497 | 9752 |
1 | 798400 | rs10900604 | A | G | -0.0930 | 0.0760 | 0.2209999 | 0.2210714 | NA | 0.410543 | 9983 |
1 | 798959 | rs11240777 | G | A | -0.0730 | 0.0678 | 0.2818000 | 0.2816160 | NA | 0.409944 | 11550 |
1 | 801467 | rs61768212 | G | C | -0.1094 | 0.0931 | 0.2398999 | 0.2399625 | NA | 0.193091 | 9555 |
1 | 804759 | rs7526310 | C | T | -0.1252 | 0.0930 | 0.1780000 | 0.1782262 | NA | 0.193890 | 9555 |
1 | 808631 | rs11240779 | G | A | 0.0336 | 0.0720 | 0.6404998 | 0.6407384 | NA | 0.453474 | 9983 |
1 | 808928 | rs11240780 | C | T | 0.0308 | 0.0722 | 0.6696995 | 0.6696759 | NA | 0.452276 | 9983 |
1 | 845635 | rs117086422 | C | T | -0.0091 | 0.0690 | 0.8954000 | 0.8950760 | NA | 0.158546 | 11550 |
1 | 845938 | rs57760052 | G | A | 0.0126 | 0.0689 | 0.8552000 | 0.8548971 | NA | 0.363419 | 11550 |
1 | 846078 | rs28612348 | C | T | -0.0300 | 0.0713 | 0.6737007 | 0.6739323 | NA | 0.161741 | 11550 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51213613 | rs34726907 | C | T | 0.1124 | 0.0986 | 0.2540002 | 0.2543032 | NA | 0.1727240 | 7948 |
22 | 51216564 | rs9616970 | T | C | 0.1034 | 0.0985 | 0.2938001 | 0.2938348 | NA | 0.1563500 | 7948 |
22 | 51217954 | rs9616974 | G | A | 0.1348 | 0.1256 | 0.2833003 | 0.2831597 | NA | 0.0621006 | 7751 |
22 | 51218224 | rs9616975 | C | A | 0.1348 | 0.1256 | 0.2833003 | 0.2831597 | NA | 0.0619010 | 7751 |
22 | 51218377 | rs2519461 | G | C | 0.1446 | 0.1258 | 0.2503001 | 0.2503731 | NA | 0.0826677 | 7751 |
22 | 51219387 | rs9616832 | T | C | 0.1345 | 0.1256 | 0.2838997 | 0.2842324 | NA | 0.0654952 | 7751 |
22 | 51221731 | rs115055839 | T | C | 0.1347 | 0.1261 | 0.2855999 | 0.2854304 | NA | 0.0625000 | 7751 |
22 | 51222100 | rs114553188 | G | T | -0.0064 | 0.1518 | 0.9666000 | 0.9663706 | NA | 0.0880591 | 7787 |
22 | 51223637 | rs375798137 | G | A | -0.0344 | 0.1529 | 0.8220000 | 0.8219920 | NA | 0.0788738 | 7787 |
22 | 51229805 | rs9616985 | T | C | 0.1381 | 0.1262 | 0.2737997 | 0.2738257 | NA | 0.0730831 | 7751 |
1 797440 rs58013264 T C . PASS . ES:SE:LP:SS:ID -0.1021:0.0925:0.568797:9752:rs58013264
1 798400 rs10900604 A G . PASS . ES:SE:LP:SS:ID -0.093:0.076:0.655608:9983:rs10900604
1 798959 rs11240777 G A . PASS . ES:SE:LP:SS:ID -0.073:0.0678:0.550059:11550:rs11240777
1 801467 rs61768212 G C . PASS . ES:SE:LP:SS:ID -0.1094:0.0931:0.61997:9555:rs61768212
1 804759 rs7526310 C T . PASS . ES:SE:LP:SS:ID -0.1252:0.093:0.74958:9555:rs7526310
1 808631 rs11240779 G A . PASS . ES:SE:LP:SS:ID 0.0336:0.072:0.193481:9983:rs11240779
1 808928 rs1247187939 C T . PASS . ES:SE:LP:SS:ID 0.0308:0.0722:0.17412:9983:rs1247187939
1 845635 rs117086422 C T . PASS . ES:SE:LP:SS:ID -0.0091:0.069:0.0479829:11550:rs117086422
1 845938 rs57760052 G A . PASS . ES:SE:LP:SS:ID 0.0126:0.0689:0.0679323:11550:rs57760052
1 846078 rs778265812 C T . PASS . ES:SE:LP:SS:ID -0.03:0.0713:0.171533:11550:rs778265812
1 846398 rs58781670 G A . PASS . ES:SE:LP:SS:ID 0.0201:0.0694:0.112383:11550:rs58781670
1 846808 rs4475691 C T . PASS . ES:SE:LP:SS:ID -0.0306:0.071:0.17633:11550:rs4475691
1 846864 rs1269142199 G C . PASS . ES:SE:LP:SS:ID -0.0401:0.0713:0.241391:11550:rs1269142199
1 847228 rs3905286 C T . PASS . ES:SE:LP:SS:ID -0.0026:0.0699:0.0128255:11550:rs3905286
1 847491 rs1158719307 G A . PASS . ES:SE:LP:SS:ID 0.0185:0.0687:0.103694:11550:rs1158719307
1 848090 rs4246505 G A . PASS . ES:SE:LP:SS:ID 0.0082:0.0688:0.0431595:11550:rs4246505
1 848445 rs1156895099 G A . PASS . ES:SE:LP:SS:ID 0.0211:0.0688:0.119815:11550:rs1156895099
1 848456 rs11507767 A G . PASS . ES:SE:LP:SS:ID 0.0207:0.0688:0.117077:11550:rs11507767
1 848738 rs3829741 C T . PASS . ES:SE:LP:SS:ID 0.0096:0.0688:0.050854:11550:rs3829741
1 850062 rs28723578 A T . PASS . ES:SE:LP:SS:ID 0.0126:0.0686:0.0684404:11550:rs28723578
1 850123 rs28622257 C T . PASS . ES:SE:LP:SS:ID 0.0079:0.0689:0.0414361:11550:rs28622257
1 851190 rs28609852 G A . PASS . ES:SE:LP:SS:ID 0.0188:0.0687:0.105684:11550:rs28609852
1 851204 rs28552953 G C . PASS . ES:SE:LP:SS:ID 0.022:0.0679:0.127145:11550:rs28552953
1 852664 rs28605311 C T . PASS . ES:SE:LP:SS:ID 0.0187:0.0695:0.103253:11550:rs28605311
1 852758 rs4970462 G C . PASS . ES:SE:LP:SS:ID 0.0178:0.0695:0.098106:11550:rs4970462
1 853239 rs4970380 A G . PASS . ES:SE:LP:SS:ID 0.0186:0.0695:0.102923:11550:rs4970380
1 854250 rs7537756 A G . PASS . ES:SE:LP:SS:ID 0.0211:0.0693:0.118615:11550:rs7537756
1 856476 rs4040605 A G . PASS . ES:SE:LP:SS:ID -0.0454:0.0635:0.32413:9983:rs4040605
1 858040 rs4970460 C A . PASS . ES:SE:LP:SS:ID 0.1357:0.0764:1.12085:9983:rs4970460
1 858051 rs4970459 C T . PASS . ES:SE:LP:SS:ID 0.1343:0.0763:1.1048:9983:rs4970459
1 858801 rs7418179 A G . PASS . ES:SE:LP:SS:ID -0.1614:0.0735:1.55191:9983:rs7418179
1 860416 rs61464428 G A . PASS . ES:SE:LP:SS:ID -0.1789:0.0734:1.82798:9983:rs61464428
1 860688 rs60837925 G A . PASS . ES:SE:LP:SS:ID -0.1804:0.0734:1.85263:9983:rs60837925
1 861630 rs2879816 G A . PASS . ES:SE:LP:SS:ID -0.1799:0.0735:1.84436:9983:rs2879816
1 862866 rs3892970 C T . PASS . ES:SE:LP:SS:ID -0.1763:0.0732:1.79697:9983:rs3892970
1 864002 rs1806501 G C . PASS . ES:SE:LP:SS:ID 0.1747:0.0754:1.68952:9983:rs1806501
1 864938 rs1185651409 G A . PASS . ES:SE:LP:SS:ID -0.151:0.0724:1.43121:9983:rs1185651409
1 865219 rs75551395 G A . PASS . ES:SE:LP:SS:ID 0.13:0.0753:1.075:9983:rs75551395
1 866893 rs2880024 T C . PASS . ES:SE:LP:SS:ID 0.0211:0.0614:0.135845:9983:rs2880024
1 866938 rs74047407 G A . PASS . ES:SE:LP:SS:ID 0.1588:0.0733:1.51999:9983:rs74047407
1 867635 rs76964081 C T . PASS . ES:SE:LP:SS:ID 0.1422:0.0751:1.23381:9983:rs76964081
1 870645 rs28576697 T C . PASS . ES:SE:LP:SS:ID 0.0491:0.0673:0.331707:9983:rs28576697
1 871334 rs4072383 G T . PASS . ES:SE:LP:SS:ID -0.0567:0.0672:0.399245:9983:rs4072383
1 872352 rs1445142858 G C . PASS . ES:SE:LP:SS:ID 0.0425:0.0686:0.270835:9983:rs1445142858
1 873558 rs1110052 G T . PASS . ES:SE:LP:SS:ID -0.0379:0.0669:0.24306:9983:rs1110052
1 875770 rs4970379 A G . PASS . ES:SE:LP:SS:ID 0.0168:0.0619:0.104688:9983:rs4970379
1 876499 rs755331663 A G . PASS . ES:SE:LP:SS:ID 0.0481:0.1315:0.146119:9689:rs755331663
1 877147 rs114982608 G A . PASS . ES:SE:LP:SS:ID 0.0452:0.0698:0.286341:9983:rs114982608
1 879676 rs6605067 G A . PASS . ES:SE:LP:SS:ID 0.0286:0.1296:0.0832829:9689:rs6605067
1 879687 rs2839 T C . PASS . ES:SE:LP:SS:ID 0.0459:0.1315:0.138406:9689:rs2839