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-97,TotalVariants=7506485,VariantsNotRead=6849,HarmonisedVariants=7296260,VariantsNotHarmonised=203376,SwitchedAlleles=60812,NormalisedVariants=0,TotalControls=2329,TotalCases=1119,StudyType=CaseControl>",
    "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/fe955091-7af8-4eab-81ec-938e5864be46/call-vcf/inputs/562856380/upload.txt.gz --id ieu-b-97 --json /data/cromwell-executions/qc/fe955091-7af8-4eab-81ec-938e5864be46/call-vcf/inputs/562856380/ieu-b-97_data.json --ref /data/cromwell-executions/qc/fe955091-7af8-4eab-81ec-938e5864be46/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/fe955091-7af8-4eab-81ec-938e5864be46/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-97/ieu-b-97.vcf.gz --alias alias.txt --cohort_cases 1119 --cohort_controls 2329; 1.3.0",
    "file_date": "2020-12-18T00:56:39.712169",
    "bcftools_viewVersion": "1.9+htslib-1.9",
    "bcftools_viewCommand": "view -h /data/cromwell-executions/qc/fe955091-7af8-4eab-81ec-938e5864be46/call-report/inputs/562856380/ieu-b-97.vcf.gz; Date=Fri Dec 18 01:16:52 2020"
}

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/fe955091-7af8-4eab-81ec-938e5864be46/call-ldsc/inputs/562856380/ieu-b-97.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-97/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Dec 18 01:08:52 2020
Reading summary statistics from /data/cromwell-executions/qc/fe955091-7af8-4eab-81ec-938e5864be46/call-ldsc/inputs/562856380/ieu-b-97.vcf.gz ...
Read summary statistics for 7295370 SNPs.
Dropped 20617 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, 1102806 SNPs remain.
After merging with regression SNP LD, 1102806 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.178 (0.1304)
Lambda GC: 1.0291
Mean Chi^2: 1.021
Intercept: 1.0088 (0.0065)
Ratio: 0.4202 (0.311)
Analysis finished at Fri Dec 18 01:10:18 2020
Total time elapsed: 1.0m:25.52s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9368,
    "inflation_factor": 1.0311,
    "mean_EFFECT": -0.0001,
    "n": 3448,
    "n_snps": 7296260,
    "n_clumped_hits": 1,
    "n_p_sig": 1,
    "n_mono": 3343,
    "n_ns": 0,
    "n_mac": 2930,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 64170,
    "n_est": 3344.0361,
    "ratio_se_n": 0.9848,
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": 2.3405,
    "sd_y_est2": 2.305,
    "r2_sum1": 0.0551,
    "r2_sum2": 0.0101,
    "r2_sum3": 0.0104,
    "r2_sum4": 0.0088,
    "ldsc_nsnp_merge_refpanel_ld": 1102806,
    "ldsc_nsnp_merge_regression_ld": 1102806,
    "ldsc_observed_scale_h2_beta": 0.178,
    "ldsc_observed_scale_h2_se": 0.1304,
    "ldsc_intercept_beta": 1.0088,
    "ldsc_intercept_se": 0.0065,
    "ldsc_lambda_gc": 1.0291,
    "ldsc_mean_chisq": 1.021,
    "ldsc_ratio": 0.419
}

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 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

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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 874 0.9998802 3 58 0 7295303 0 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
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.648628e+00 5.753559e+00 1.000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.875257e+07 5.640889e+07 828.000 3.227813e+07 6.931453e+07 1.146225e+08 2.492164e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.336000e-04 5.370683e-01 -6.908 -6.100000e-02 0.000000e+00 6.100000e-02 5.959870e+02 ▇▁▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.142127e-01 6.612754e-01 0.052 6.100000e-02 8.300000e-02 1.420000e-01 7.456310e+02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.954778e-01 2.892346e-01 0.000 2.438983e-01 4.934089e-01 7.457805e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.955163e-01 2.892742e-01 0.000 2.440857e-01 4.934811e-01 7.459807e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.603347e-01 2.623900e-01 0.000 4.600000e-02 1.560000e-01 4.100000e-01 1.000000e+00 ▇▂▂▁▁
numeric AF_reference 64170 0.9912051 NA NA NA NA NA 2.597271e-01 2.523694e-01 0.000 5.491210e-02 1.697280e-01 4.029550e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.447901e+03 2.408132e+00 3220.000 3.448000e+03 3.448000e+03 3.448000e+03 3.448000e+03 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 693731 rs12238997 A G 0.049 0.138 0.7227765 0.7225353 0.126 0.141773 3448
1 729679 rs4951859 C G -0.057 0.126 0.6512309 0.6509946 0.822 0.639976 3448
1 731718 rs142557973 T C 0.049 0.125 0.6981054 0.6950582 0.133 0.154353 3448
1 734349 rs141242758 T C 0.054 0.125 0.6604577 0.6657414 0.132 0.152556 3448
1 752566 rs3094315 G A 0.007 0.074 0.9280001 0.9246368 0.812 0.718251 3448
1 752721 rs3131972 A G 0.000 0.073 0.9967000 1.0000000 0.809 0.653355 3447
1 753405 rs3115860 C A -0.024 0.113 0.8275396 0.8318033 0.854 0.751797 3448
1 753541 rs2073813 G A 0.023 0.112 0.8372323 0.8372931 0.148 0.301917 3448
1 754182 rs3131969 A G -0.024 0.112 0.8258584 0.8303243 0.851 0.678514 3448
1 754192 rs3131968 A G -0.024 0.112 0.8264082 0.8303243 0.851 0.678514 3448
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51218224 rs9616975 C A -0.021 0.162 0.8962936 0.8968595 0.073 0.0619010 3448
22 51218377 rs2519461 G C -0.026 0.161 0.8692758 0.8717069 0.075 0.0826677 3448
22 51219006 rs28729663 G A 0.086 0.118 0.4656183 0.4661157 0.139 0.2052720 3448
22 51219387 rs9616832 T C -0.031 0.163 0.8448918 0.8491649 0.074 0.0654952 3448
22 51219704 rs147475742 G A 0.165 0.229 0.4719794 0.4712024 0.041 0.0473243 3448
22 51221731 rs115055839 T C -0.019 0.164 0.9057791 0.9077685 0.073 0.0625000 3448
22 51222100 rs114553188 G T 0.087 0.174 0.6156176 0.6170751 0.056 0.0880591 3448
22 51223637 rs375798137 G A 0.088 0.175 0.6165524 0.6150647 0.055 0.0788738 3448
22 51229805 rs9616985 T C -0.012 0.166 0.9423054 0.9423718 0.073 0.0730831 3448
22 51237063 rs3896457 T C 0.024 0.099 0.8123220 0.8084515 0.287 0.2050720 3448

bcf preview

1   693731  rs12238997  A   G   .   PASS    AF=0.126    ES:SE:LP:AF:SS:SI:NC:ID 0.049:0.138:0.140996:0.126:3448:0.324:1119:rs12238997
1   729679  rs4951859   C   G   .   PASS    AF=0.822    ES:SE:LP:AF:SS:SI:NC:ID -0.057:0.126:0.186265:0.822:3448:0.361:1119:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.133    ES:SE:LP:AF:SS:SI:NC:ID 0.049:0.125:0.156079:0.133:3448:0.378:1119:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.132    ES:SE:LP:AF:SS:SI:NC:ID 0.054:0.125:0.180155:0.132:3448:0.379:1119:rs141242758
1   752566  rs3094315   G   A   .   PASS    AF=0.812    ES:SE:LP:AF:SS:SI:NC:ID 0.007:0.074:0.032452:0.812:3448:1:1119:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.809    ES:SE:LP:AF:SS:SI:NC:ID -0:0.073:0.00143554:0.809:3447:1:1119:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.854    ES:SE:LP:AF:SS:SI:NC:ID -0.024:0.113:0.0822112:0.854:3448:0.473:1119:rs3115860
1   753541  rs1388595942    G   A   .   PASS    AF=0.148    ES:SE:LP:AF:SS:SI:NC:ID 0.023:0.112:0.077154:0.148:3448:0.481:1119:rs1388595942
1   754182  rs3131969   A   G   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID -0.024:0.112:0.0830944:0.851:3448:0.493:1119:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID -0.024:0.112:0.0828054:0.851:3448:0.494:1119:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID -0.025:0.112:0.0872692:0.851:3448:0.494:1119:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.817    ES:SE:LP:AF:SS:SI:NC:ID -0.038:0.115:0.128109:0.817:3448:0.417:1119:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.818    ES:SE:LP:AF:SS:SI:NC:ID -0.039:0.115:0.134664:0.818:3448:0.42:1119:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.822    ES:SE:LP:AF:SS:SI:NC:ID -0.042:0.116:0.143235:0.822:3448:0.403:1119:rs3131965
1   755890  rs1280367067    A   T   .   PASS    AF=0.853    ES:SE:LP:AF:SS:SI:NC:ID -0.023:0.112:0.076661:0.853:3448:0.48:1119:rs1280367067
1   756604  rs3131962   A   G   .   PASS    AF=0.853    ES:SE:LP:AF:SS:SI:NC:ID -0.021:0.112:0.0718582:0.853:3448:0.482:1119:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.848    ES:SE:LP:AF:SS:SI:NC:ID -0.023:0.11:0.0799864:0.848:3448:0.525:1119:rs3115853
1   757734  rs1557551770    C   T   .   PASS    AF=0.853    ES:SE:LP:AF:SS:SI:NC:ID -0.022:0.112:0.0733018:0.853:3448:0.484:1119:rs1557551770
1   757936  rs1360886751    C   A   .   PASS    AF=0.853    ES:SE:LP:AF:SS:SI:NC:ID -0.022:0.112:0.0740001:0.853:3448:0.485:1119:rs1360886751
1   758144  rs3131956   A   G   .   PASS    AF=0.853    ES:SE:LP:AF:SS:SI:NC:ID -0.021:0.112:0.0721402:0.853:3448:0.485:1119:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.854    ES:SE:LP:AF:SS:SI:NC:ID -0.022:0.112:0.0744249:0.854:3448:0.484:1119:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.821    ES:SE:LP:AF:SS:SI:NC:ID -0.043:0.115:0.150657:0.821:3448:0.408:1119:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.821    ES:SE:LP:AF:SS:SI:NC:ID -0.043:0.114:0.149525:0.821:3448:0.409:1119:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.843    ES:SE:LP:AF:SS:SI:NC:ID -0.029:0.109:0.105454:0.843:3448:0.532:1119:rs2286139
1   766007  rs61768174  A   C   .   PASS    AF=0.11 ES:SE:LP:AF:SS:SI:NC:ID 0.109:0.12:0.440082:0.11:3448:0.458:1119:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.731    ES:SE:LP:AF:SS:SI:NC:ID 0.035:0.076:0.193276:0.731:3448:0.651:1119:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.119    ES:SE:LP:AF:SS:SI:NC:ID -0.149:0.13:0.593322:0.119:3448:0.395:1119:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.012    ES:SE:LP:AF:SS:SI:NC:ID -0.082:0.428:0.0720029:0.012:3448:0.332:1119:rs12562811
1   769223  rs60320384  C   G   .   PASS    AF=0.144    ES:SE:LP:AF:SS:SI:NC:ID 0.034:0.109:0.121617:0.144:3448:0.491:1119:rs60320384
1   770377  rs112563271 A   T   .   PASS    AF=0.013    ES:SE:LP:AF:SS:SI:NC:ID -0.414:0.31:0.740167:0.013:3447:1:1119:rs112563271
1   771823  rs2977605   T   C   .   PASS    AF=0.854    ES:SE:LP:AF:SS:SI:NC:ID -0.028:0.108:0.102718:0.854:3448:0.517:1119:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.145    ES:SE:LP:AF:SS:SI:NC:ID 0.031:0.108:0.112602:0.145:3448:0.5:1119:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.854    ES:SE:LP:AF:SS:SI:NC:ID -0.029:0.107:0.104337:0.854:3448:0.521:1119:rs2905039
1   777122  rs2980319   A   T   .   PASS    AF=0.855    ES:SE:LP:AF:SS:SI:NC:ID -0.013:0.107:0.0445298:0.855:3448:0.528:1119:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.102    ES:SE:LP:AF:SS:SI:NC:ID -0.151:0.135:0.579437:0.102:3448:0.426:1119:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.143    ES:SE:LP:AF:SS:SI:NC:ID 0.014:0.108:0.046378:0.143:3448:0.513:1119:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.144    ES:SE:LP:AF:SS:SI:NC:ID 0.01:0.107:0.0327055:0.144:3448:0.522:1119:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID -0.007:0.105:0.023187:0.851:3448:0.563:1119:rs2977612
1   781845  rs1391043716    A   G   .   PASS    AF=0.106    ES:SE:LP:AF:SS:SI:NC:ID 0.09:0.118:0.347208:0.106:3448:0.485:1119:rs1391043716
1   782981  rs6594026   C   T   .   PASS    AF=0.147    ES:SE:LP:AF:SS:SI:NC:ID 0.009:0.105:0.0309262:0.147:3448:0.552:1119:rs6594026
1   785050  rs2905062   G   A   .   PASS    AF=0.85 ES:SE:LP:AF:SS:SI:NC:ID -0.013:0.103:0.0447148:0.85:3448:0.606:1119:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.85 ES:SE:LP:AF:SS:SI:NC:ID -0.014:0.103:0.0489316:0.85:3448:0.609:1119:rs2980300
1   787399  rs2905055   G   T   .   PASS    AF=0.844    ES:SE:LP:AF:SS:SI:NC:ID -0.019:0.104:0.0686491:0.844:3448:0.579:1119:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.144    ES:SE:LP:AF:SS:SI:NC:ID 0.011:0.105:0.0366453:0.144:3448:0.544:1119:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.843    ES:SE:LP:AF:SS:SI:NC:ID -0.026:0.103:0.0961035:0.843:3448:0.587:1119:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID -0.017:0.103:0.0608377:0.851:3448:0.605:1119:rs2905053
1   790465  rs61768207  G   A   .   PASS    AF=0.104    ES:SE:LP:AF:SS:SI:NC:ID 0.094:0.118:0.370681:0.104:3448:0.522:1119:rs61768207
1   791191  rs111818025 G   A   .   PASS    AF=0.143    ES:SE:LP:AF:SS:SI:NC:ID 0.009:0.104:0.032182:0.143:3448:0.549:1119:rs111818025
1   791853  rs6684487   G   A   .   PASS    AF=0.102    ES:SE:LP:AF:SS:SI:NC:ID -0.142:0.128:0.565618:0.102:3448:0.481:1119:rs6684487
1   794332  rs12127425  G   A   .   PASS    AF=0.089    ES:SE:LP:AF:SS:SI:NC:ID -0.17:0.129:0.725891:0.089:3448:0.552:1119:rs12127425