Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_plot

beta_std plot

beta_std_plot

Metadata

{
    "fileformat": "VCFv4.2",
    "FILTER": "<ID=PASS,Description=\"All filters passed\">",
    "INFO": "<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">",
    "FORMAT": "<ID=ES,Number=A,Type=Float,Description=\"Effect size estimate relative to the alternative allele\">",
    "FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
    "FORMAT.2": "<ID=LP,Number=A,Type=Float,Description=\"-log10 p-value for effect estimate\">",
    "FORMAT.3": "<ID=AF,Number=A,Type=Float,Description=\"Alternate allele frequency in the association study\">",
    "FORMAT.4": "<ID=SS,Number=A,Type=Float,Description=\"Sample size used to estimate genetic effect\">",
    "FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
    "FORMAT.6": "<ID=SI,Number=A,Type=Float,Description=\"Accuracy score of summary data imputation\">",
    "FORMAT.7": "<ID=NC,Number=A,Type=Float,Description=\"Number of cases used to estimate genetic effect\">",
    "FORMAT.8": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
    "META": "<ID=TotalVariants,Number=1,Type=Integer,Description=\"Total number of variants in input\">",
    "META.1": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
    "META.2": "<ID=HarmonisedVariants,Number=1,Type=Integer,Description=\"Total number of harmonised variants\">",
    "META.3": "<ID=VariantsNotHarmonised,Number=1,Type=Integer,Description=\"Total number of variants that could not be harmonised\">",
    "META.4": "<ID=SwitchedAlleles,Number=1,Type=Integer,Description=\"Total number of variants strand switched\">",
    "META.5": "<ID=TotalControls,Number=1,Type=Integer,Description=\"Total number of controls in the association study\">",
    "META.6": "<ID=TotalCases,Number=1,Type=Integer,Description=\"Total number of cases in the association study\">",
    "META.7": "<ID=StudyType,Number=1,Type=String,Description=\"Type of GWAS study [Continuous or CaseControl]\">",
    "SAMPLE": "<ID=ieu-b-5121,TotalVariants=12216219,VariantsNotRead=747001,HarmonisedVariants=11469218,VariantsNotHarmonised=0,SwitchedAlleles=11032187,NormalisedVariants=0,StudyType=Continuous>",
    "contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
    "contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
    "contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
    "contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
    "contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
    "contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
    "contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
    "contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
    "contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
    "contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
    "contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
    "contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
    "contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
    "contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
    "contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
    "contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
    "contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
    "contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
    "contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
    "contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
    "contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
    "contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
    "contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
    "contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
    "contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
    "contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
    "contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
    "contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
    "contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
    "contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
    "contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
    "contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
    "contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
    "contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
    "contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
    "contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
    "contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
    "contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
    "contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
    "contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
    "contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
    "contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
    "contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
    "contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
    "contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
    "contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
    "contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
    "contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
    "contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
    "contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
    "contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
    "contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
    "contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
    "contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
    "contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
    "contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
    "contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
    "contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
    "contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
    "contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
    "contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
    "contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
    "contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
    "contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
    "contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
    "contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
    "contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
    "contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
    "contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
    "contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
    "contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
    "contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
    "contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
    "contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
    "contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
    "contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
    "contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
    "contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
    "contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
    "contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
    "contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
    "contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
    "contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
    "contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
    "Gwas2VCF_command": "--data /data/cromwell-executions/qc/b8566d6c-284b-4ad9-9759-6c50e3d1cb73/call-vcf/inputs/-261021447/upload.txt.gz --id ieu-b-5121 --json /data/cromwell-executions/qc/b8566d6c-284b-4ad9-9759-6c50e3d1cb73/call-vcf/inputs/-261021447/ieu-b-5121_data.json --ref /data/cromwell-executions/qc/b8566d6c-284b-4ad9-9759-6c50e3d1cb73/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/b8566d6c-284b-4ad9-9759-6c50e3d1cb73/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-5121/ieu-b-5121.vcf.gz --alias alias.txt; 1.3.0",
    "file_date": "2024-01-20T16:42:47.068252",
    "bcftools_viewVersion": "1.9+htslib-1.9",
    "bcftools_viewCommand": "view -h /data/cromwell-executions/qc/b8566d6c-284b-4ad9-9759-6c50e3d1cb73/call-report/inputs/-261021447/ieu-b-5121.vcf.gz; Date=Sat Jan 20 17:09:06 2024"
}

LDSC

*********************************************************************
* 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/b8566d6c-284b-4ad9-9759-6c50e3d1cb73/call-ldsc/inputs/-261021447/ieu-b-5121.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5121/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Sat Jan 20 16:58:33 2024
Reading summary statistics from /data/cromwell-executions/qc/b8566d6c-284b-4ad9-9759-6c50e3d1cb73/call-ldsc/inputs/-261021447/ieu-b-5121.vcf.gz ...
Read summary statistics for 0 SNPs.
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.
Traceback (most recent call last):
  File "./ldsc/ldsc.py", line 647, in <module>
    sumstats.estimate_h2(args, log)
  File "/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
    args, log, args.h2)
  File "/ldsc/ldscore/sumstats.py", line 252, in _read_ld_sumstats
    sumstats = _merge_and_log(ref_ld, sumstats, 'reference panel LD', log)
  File "/ldsc/ldscore/sumstats.py", line 238, in _merge_and_log
    raise ValueError(msg.format(N=len(sumstats), F=noun))
ValueError: After merging with reference panel LD, 0 SNPs remain.

Analysis finished at Sat Jan 20 16:59:43 2024
Total time elapsed: 1.0m:9.92s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9505,
    "inflation_factor": 1.0475,
    "mean_EFFECT": 0.0027,
    "n": "-Inf",
    "n_snps": 11469218,
    "n_clumped_hits": 4,
    "n_p_sig": 195,
    "n_mono": 0,
    "n_ns": 529292,
    "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": 693417,
    "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": 0,
    "ldsc_nsnp_merge_regression_ld": "NA",
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": "NA",
    "ldsc_intercept_se": "NA",
    "ldsc_lambda_gc": "NA",
    "ldsc_mean_chisq": "NA",
    "ldsc_ratio": "NA"
}

Flags

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 NA
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio NA
ldsc_intercept_beta NA
n_clumped_hits FALSE
r2_sum1 FALSE
r2_sum2 FALSE
r2_sum3 FALSE
r2_sum4 FALSE

Definitions

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 SNPs
  • n_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:
    • alleles other than A, C, G or T.
    • P-values < 0 or > 1.
    • negative or infinite standard errors (<= 0 or = Infinity).
    • infinite beta estimates or allele frequencies < 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.
    • \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
    • \({z}_j = \frac{\beta_j}{{se}_j}\),
    • and \(\beta_j\) is the reported effect size.
  • 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.
    • \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
    • \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
  • 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.
    • \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
    • \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
    • and \({se}_j\) is the reported standard error.
  • 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.
    • \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
    • \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),

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 > 0.5
  • ldsc_intercept_beta: ldsc_intercept_beta > 1.5
  • n_clumped_hits: n_clumped_hits > 1000
  • r2_sum<*>: r2_sum<*> > 0.5

Plots

  • Manhattan plot
    • Red line: \(-log_{10}^{5 \times 10^{-8}}\)
    • Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
  • QQ plot
  • AF plot
  • P-Z plot
  • beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)

Diagnostics

Details

Summary stats

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 586 0.9999489 3 58 0 11443864 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 4 0 340 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 4 0 340 0 NA NA NA NA NA NA NA NA NA NA
logical N 11469218 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 8.630471e+00 5.755513e+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 7.864496e+07 5.630108e+07 302.0000000 3.246429e+07 6.907161e+07 1.143027e+08 2.492405e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 2.723700e-03 3.156019e-01 -5.5792400 -9.194230e-02 1.359900e-03 9.585050e-02 5.063510e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 2.263418e-01 2.185496e-01 0.0642329 7.801950e-02 1.276010e-01 2.953360e-01 3.690690e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.944462e-01 2.904585e-01 0.0000000 2.399999e-01 4.899999e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.944458e-01 2.904329e-01 0.0000000 2.413062e-01 4.924710e-01 7.463138e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.258873e-01 2.758449e-01 0.0003960 1.446300e-02 9.182400e-02 3.638950e-01 9.995130e-01 ▇▂▁▁▁
numeric AF_reference 693417 0.9395410 NA NA NA NA NA NA NA 2.098983e-01 2.494755e-01 0.0000000 1.178120e-02 1.028350e-01 3.296730e-01 1.000000e+00 ▇▂▁▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10177 rs1264289758 AC A -0.0557598 0.0989684 0.5700002 0.5731556 0.598523 NA NA
1 10352 rs1557426776 TA T -0.1222350 0.1024410 0.2300001 0.2327819 0.606283 NA NA
1 11008 rs575272151 C G -0.0774514 0.1703310 0.6499995 0.6493171 0.085719 0.0880591 NA
1 11012 rs544419019 C G -0.0774514 0.1703310 0.6499995 0.6493171 0.085719 0.0880591 NA
1 13110 rs540538026 G A 0.2095400 0.2297110 0.3599996 0.3616689 0.057845 0.0267572 NA
1 13116 rs62635286 T G 0.0342927 0.1346710 0.8000000 0.7990007 0.187909 0.0970447 NA
1 13118 rs200579949 A G 0.0342927 0.1346710 0.8000000 0.7990007 0.187909 0.0970447 NA
1 13273 rs531730856 G C 0.0488450 0.1588850 0.7600007 0.7585210 0.131847 0.0950479 NA
1 14464 rs546169444 A T 0.1417950 0.1423280 0.3200000 0.3191262 0.157618 0.0958466 NA
1 14599 rs531646671 T A 0.1784730 0.1305970 0.1700000 0.1717528 0.191172 0.1475640 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51233182 rs4040317 G A -0.1197060 0.0811466 0.1400000 0.1401636 0.320182 0.2633790 NA
22 51233300 rs9616839 C T -0.1282280 0.0807872 0.1100001 0.1124602 0.334846 0.3146960 NA
22 51233312 rs62240043 A G -0.1512740 0.0854602 0.0769999 0.0767087 0.272584 0.2134580 NA
22 51233347 rs62240044 T C -0.1512740 0.0854602 0.0769999 0.0767087 0.272584 0.2134580 NA
22 51234799 rs191117135 G A -0.1504970 0.3052110 0.6200004 0.6219478 0.015494 0.0059904 NA
22 51235959 rs200189535 T C 0.1767270 0.1001190 0.0779992 0.0775353 0.193099 0.1996810 NA
22 51235979 rs62240045 G A 0.0714018 0.1112370 0.5199996 0.5209453 0.262206 0.2400160 NA
22 51236013 rs200507571 AT A -0.0202440 0.0860347 0.8100000 0.8139756 0.748262 NA NA
22 51237063 rs3896457 T C -0.1473070 0.0785223 0.0610000 0.0606567 0.299277 0.2050720 NA
22 51237712 rs370652263 G A -0.1894090 0.1578300 0.2300001 0.2301074 0.053946 0.0690895 NA

bcf preview

1   10177   rs1264289758    AC  A   .   PASS    AF=0.598523 ES:SE:LP:AF:SI:ID   -0.0557598:0.0989684:0.244125:0.598523:0.466089:rs1264289758
1   10352   rs1557426776    TA  T   .   PASS    AF=0.606283 ES:SE:LP:AF:SI:ID   -0.122235:0.102441:0.638272:0.606283:0.44449:rs1557426776
1   11008   rs575272151 C   G   .   PASS    AF=0.085719 ES:SE:LP:AF:SI:ID   -0.0774514:0.170331:0.187087:0.085719:0.486664:rs575272151
1   11012   rs544419019 C   G   .   PASS    AF=0.085719 ES:SE:LP:AF:SI:ID   -0.0774514:0.170331:0.187087:0.085719:0.486664:rs544419019
1   13110   rs540538026 G   A   .   PASS    AF=0.057845 ES:SE:LP:AF:SI:ID   0.20954:0.229711:0.443698:0.057845:0.39209:rs540538026
1   13116   rs62635286  T   G   .   PASS    AF=0.187909 ES:SE:LP:AF:SI:ID   0.0342927:0.134671:0.09691:0.187909:0.404681:rs62635286
1   13118   rs62028691  A   G   .   PASS    AF=0.187909 ES:SE:LP:AF:SI:ID   0.0342927:0.134671:0.09691:0.187909:0.404681:rs62028691
1   13273   rs531730856 G   C   .   PASS    AF=0.131847 ES:SE:LP:AF:SI:ID   0.048845:0.158885:0.119186:0.131847:0.390731:rs531730856
1   14464   rs546169444 A   T   .   PASS    AF=0.157618 ES:SE:LP:AF:SI:ID   0.141795:0.142328:0.49485:0.157618:0.410824:rs546169444
1   14599   rs707680    T   A   .   PASS    AF=0.191172 ES:SE:LP:AF:SI:ID   0.178473:0.130597:0.769551:0.191172:0.424479:rs707680
1   14604   rs1418508701    A   G   .   PASS    AF=0.191172 ES:SE:LP:AF:SI:ID   0.178473:0.130597:0.769551:0.191172:0.424479:rs1418508701
1   14930   rs6682385   A   G   .   PASS    AF=0.474146 ES:SE:LP:AF:SI:ID   -0.0470943:0.101327:0.19382:0.474146:0.437191:rs6682385
1   14933   rs199856693 G   A   .   PASS    AF=0.045168 ES:SE:LP:AF:SI:ID   0.33124:0.249841:0.744727:0.045168:0.420325:rs199856693
1   15211   rs3982632   T   G   .   PASS    AF=0.740986 ES:SE:LP:AF:SI:ID   0.0241104:0.116954:0.0757207:0.740986:0.425958:rs3982632
1   15820   rs1316988498    G   T   .   PASS    AF=0.276887 ES:SE:LP:AF:SI:ID   -0.104507:0.118647:0.420216:0.276887:0.388846:rs1316988498
1   15903   rs557514207 GC  G   .   PASS    AF=0.58162  ES:SE:LP:AF:SI:ID   -0.0336142:0.0985085:0.136677:0.58162:0.465698:rs557514207
1   28590   rs1344649620    T   TTGG    .   PASS    AF=0.957286 ES:SE:LP:AF:SI:ID   0.463882:0.281852:1:0.957286:0.339465:rs1344649620
1   30923   rs1165072081    G   T   .   PASS    AF=0.909237 ES:SE:LP:AF:SI:ID   0.177139:0.18582:0.468521:0.909237:0.391908:rs1165072081
1   47159   rs540662756 T   C   .   PASS    AF=0.063091 ES:SE:LP:AF:SI:ID   -0.211137:0.210096:0.508638:0.063091:0.418452:rs540662756
1   49298   rs10399793  T   C   .   PASS    AF=0.626616 ES:SE:LP:AF:SI:ID   0.0249699:0.118402:0.0809219:0.626616:0.338912:rs10399793
1   49554   rs539322794 A   G   .   PASS    AF=0.093244 ES:SE:LP:AF:SI:ID   0.0512426:0.182586:0.107905:0.093244:0.397311:rs539322794
1   51479   rs116400033 T   A   .   PASS    AF=0.213388 ES:SE:LP:AF:SI:ID   0.0458406:0.126561:0.142668:0.213388:0.412646:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.155533 ES:SE:LP:AF:SI:ID   0.0724566:0.141006:0.21467:0.155533:0.420773:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.397269 ES:SE:LP:AF:SI:ID   0.0172735:0.117318:0.0555173:0.397269:0.337096:rs2462492
1   54712   rs573184866 TTTT    T   .   PASS    AF=0.416318 ES:SE:LP:AF:SI:ID   -0.0735558:0.0928646:0.366532:0.416318:0.532876:rs573184866
1   54716   rs1166278911    C   T   .   PASS    AF=0.417224 ES:SE:LP:AF:SI:ID   0.128336:0.10734:0.638272:0.417224:0.39825:rs1166278911
1   55545   rs28396308  C   T   .   PASS    AF=0.253854 ES:SE:LP:AF:SI:ID   -0.269563:0.120764:1.58503:0.253854:0.404049:rs28396308
1   58814   rs114420996 G   A   .   PASS    AF=0.090624 ES:SE:LP:AF:SI:ID   -0.0570242:0.182863:0.119186:0.090624:0.402912:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.089421 ES:SE:LP:AF:SI:ID   0.0250848:0.184212:0.05061:0.089421:0.404541:rs62637815
1   60351   rs62637817  A   G   .   PASS    AF=0.081653 ES:SE:LP:AF:SI:ID   0.0384863:0.190668:0.0757207:0.081653:0.408796:rs62637817
1   62777   rs3844233   A   T   .   PASS    AF=0.43774  ES:SE:LP:AF:SI:ID   0.227696:0.101871:1.60206:0.43774:0.435397:rs3844233
1   63268   rs28664618  T   C   .   PASS    AF=0.380766 ES:SE:LP:AF:SI:ID   -0.239048:0.109866:1.52288:0.380766:0.39221:rs28664618
1   63671   rs80011619  G   A   .   PASS    AF=0.159327 ES:SE:LP:AF:SI:ID   -0.116476:0.139446:0.39794:0.159327:0.429054:rs80011619
1   64931   rs62639104  G   A   .   PASS    AF=0.080347 ES:SE:LP:AF:SI:ID   0.0385598:0.192662:0.0757207:0.080347:0.405239:rs62639104
1   68082   rs367789441 T   C   .   PASS    AF=0.070677 ES:SE:LP:AF:SI:ID   0.0826181:0.196009:0.173925:0.070677:0.439754:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.032606 ES:SE:LP:AF:SI:ID   -0.0862865:0.300816:0.113509:0.032606:0.39852:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.074296 ES:SE:LP:AF:SI:ID   0.022552:0.191915:0.0409586:0.074296:0.436196:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.753891 ES:SE:LP:AF:SI:ID   0.126118:0.123814:0.508638:0.753891:0.393859:rs200676709
1   74790   rs13328700  C   G   .   PASS    AF=0.03488  ES:SE:LP:AF:SI:ID   0.420714:0.278155:0.886057:0.03488:0.425973:rs13328700
1   74792   rs1335672253    G   A   .   PASS    AF=0.03488  ES:SE:LP:AF:SI:ID   0.420714:0.278155:0.886057:0.03488:0.425973:rs1335672253
1   76838   rs563953605 T   G   .   PASS    AF=0.077512 ES:SE:LP:AF:SI:ID   0.154519:0.197396:0.366532:0.077512:0.401276:rs563953605
1   76854   rs367666799 A   G   .   PASS    AF=0.078413 ES:SE:LP:AF:SI:ID   -0.218231:0.18707:0.619789:0.078413:0.430178:rs367666799
1   77866   rs563593912 C   T   .   PASS    AF=0.077342 ES:SE:LP:AF:SI:ID   0.156827:0.197391:0.366532:0.077342:0.40201:rs563593912
1   77874   rs62641297  G   A   .   PASS    AF=0.077342 ES:SE:LP:AF:SI:ID   0.156827:0.197391:0.366532:0.077342:0.40201:rs62641297
1   81260   rs571136476 C   T   .   PASS    AF=0.041343 ES:SE:LP:AF:SI:ID   -0.0840682:0.273521:0.119186:0.041343:0.370765:rs571136476
1   81587   rs536406113 C   T   .   PASS    AF=0.061243 ES:SE:LP:AF:SI:ID   0.127926:0.208563:0.267606:0.061243:0.444727:rs536406113
1   82163   rs139113303 G   A   .   PASS    AF=0.076404 ES:SE:LP:AF:SI:ID   -0.240814:0.189645:0.69897:0.076404:0.429704:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.07645  ES:SE:LP:AF:SI:ID   -0.246302:0.18958:0.721246:0.07645:0.429781:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.351453 ES:SE:LP:AF:SI:ID   0.20795:0.110565:1.22185:0.351453:0.399395:rs201754587
1   86028   rs114608975 T   C   .   PASS    AF=0.104873 ES:SE:LP:AF:SI:ID   0.0684145:0.184289:0.148742:0.104873:0.340979:rs114608975