Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std 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-a-1089,TotalVariants=8234065,VariantsNotRead=0,HarmonisedVariants=8234065,VariantsNotHarmonised=0,SwitchedAlleles=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>",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1089/ieu-a-1089_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T10:15:07.314817",
    "bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1089/ieu-a-1089.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1089/ieu-a-1089_data.vcf.gz; Date=Tue Feb  4 17:16:41 2020",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ieu-a-1089/ieu-a-1089.vcf.gz; Date=Sun May 10 11:25:38 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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1089/ieu-a-1089.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/ieu-a-import/processed/ieu-a-1089/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Wed Feb  5 09:21:13 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1089/ieu-a-1089.vcf.gz ...
Read summary statistics for 8234065 SNPs.
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, 1244038 SNPs remain.
After merging with regression SNP LD, 1244038 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0029 (0.0029)
Lambda GC: 1.0036
Mean Chi^2: 1.0051
Intercept: 0.9983 (0.0051)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 09:22:35 2020
Total time elapsed: 1.0m:21.55s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9391,
    "inflation_factor": 1,
    "mean_EFFECT": -0.0002,
    "n": 119688,
    "n_snps": 8234065,
    "n_clumped_hits": 1,
    "n_p_sig": 1,
    "n_mono": 0,
    "n_ns": 529643,
    "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": 125910,
    "n_est": 121787.288,
    "ratio_se_n": 1.0087,
    "mean_diff": 0.0002,
    "ratio_diff": 2.8163,
    "sd_y_est1": 2.0493,
    "sd_y_est2": 2.0672,
    "r2_sum1": 0.0006,
    "r2_sum2": 0.0001,
    "r2_sum3": 0.0001,
    "r2_sum4": 0.0003,
    "ldsc_nsnp_merge_refpanel_ld": 1244038,
    "ldsc_nsnp_merge_regression_ld": 1244038,
    "ldsc_observed_scale_h2_beta": 0.0029,
    "ldsc_observed_scale_h2_se": 0.0029,
    "ldsc_intercept_beta": 0.9983,
    "ldsc_intercept_se": 0.0051,
    "ldsc_lambda_gc": 1.0036,
    "ldsc_mean_chisq": 1.0051,
    "ldsc_ratio": -0.3333
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
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

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 0 1.0000000 3 58 0 8234065 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 51 0 29514 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 51 0 15745 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.622937e+00 5.748526e+00 1.0000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.896169e+07 5.638206e+07 302.0000 3.244396e+07 6.962347e+07 1.146657e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.924000e-04 4.298960e-02 -0.7900 -8.900000e-03 -7.500000e-05 8.700000e-03 7.100000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.756080e-02 3.319250e-02 0.0058 7.000000e-03 1.200000e-02 3.300000e-02 2.500000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.998262e-01 2.886531e-01 0.0000 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.998840e-01 2.886056e-01 0.0000 2.493627e-01 5.011208e-01 7.493895e-01 9.999997e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.700384e-01 2.643581e-01 0.0050 5.000000e-02 1.700000e-01 4.290000e-01 9.950000e-01 ▇▃▂▁▁
numeric AF_reference 125910 0.9847086 NA NA NA NA NA 2.666407e-01 2.523943e-01 0.0000 5.910540e-02 1.811100e-01 4.165340e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.181701e+05 2.423412e+03 84747.0000 1.179120e+05 1.189950e+05 1.194740e+05 1.196880e+05 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 751343 rs28544273 T A -3.5e-05 0.014 1.0000000 0.9980053 0.126 0.242612 118061
1 751488 rs200141114 GA G -1.3e-03 0.014 0.9299999 0.9260171 0.855 NA 108511
1 753405 rs3115860 C A -3.3e-03 0.013 0.8000000 0.7996144 0.872 0.751797 118301
1 753425 rs3131970 T C -3.3e-03 0.013 0.8000000 0.7996144 0.872 0.749002 118293
1 753541 rs2073813 G A 4.0e-03 0.013 0.7700005 0.7583165 0.127 0.301917 118494
1 754182 rs3131969 A G -7.5e-03 0.013 0.5700002 0.5639914 0.871 0.678514 118771
1 754192 rs3131968 A G -7.6e-03 0.013 0.5700002 0.5588064 0.871 0.678514 118768
1 754334 rs3131967 T C -8.2e-03 0.013 0.5400003 0.5281914 0.871 0.684305 118745
1 755890 rs3115858 A T -5.2e-03 0.013 0.6899999 0.6891565 0.871 0.751398 118960
1 756434 rs61768170 G C 4.3e-03 0.013 0.7400005 0.7408188 0.128 0.188498 118969
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51216051 rs376488897 A G -0.0097 0.016 0.5300002 0.5443488 0.127 0.1365810 110698
22 51216149 rs373165495 C A -0.0110 0.016 0.5000000 0.4917677 0.127 0.1361820 110718
22 51216564 rs9616970 T C -0.0110 0.016 0.4700002 0.4917677 0.127 0.1563500 110609
22 51217954 rs9616974 G A -0.0067 0.028 0.8100000 0.8108840 0.072 0.0621006 114572
22 51218224 rs9616975 C A -0.0066 0.028 0.8100000 0.8136544 0.072 0.0619010 114574
22 51218377 rs2519461 G C 0.0061 0.027 0.8200001 0.8212590 0.073 0.0826677 114510
22 51218615 rs9616976 T A 0.0063 0.027 0.8200001 0.8155026 0.073 0.0858626 114446
22 51219387 rs9616832 T C 0.0100 0.027 0.7099994 0.7111065 0.073 0.0654952 114125
22 51220249 rs9616977 A T 0.0210 0.029 0.4600002 0.4689811 0.072 0.0595048 113707
22 51220319 rs9616978 C G 0.0240 0.032 0.4500005 0.4532547 0.069 0.0397364 113600

bcf preview

1   751343  rs28544273  T   A   .   PASS    AF=0.126    ES:SE:LP:AF:SS:ID   -3.5e-05:0.014:-0:0.126:118061:rs28544273
1   751488  rs200141114 GA  G   .   PASS    AF=0.855    ES:SE:LP:AF:SS:ID   -0.0013:0.014:0.0315171:0.855:108511:rs200141114
1   753405  rs3115860   C   A   .   PASS    AF=0.872    ES:SE:LP:AF:SS:ID   -0.0033:0.013:0.09691:0.872:118301:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.872    ES:SE:LP:AF:SS:ID   -0.0033:0.013:0.09691:0.872:118293:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.004:0.013:0.113509:0.127:118494:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0075:0.013:0.244125:0.871:118771:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0076:0.013:0.244125:0.871:118768:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0082:0.013:0.267606:0.871:118745:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0052:0.013:0.161151:0.871:118960:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0043:0.013:0.130768:0.128:118969:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0069:0.013:0.221849:0.87:119688:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869    ES:SE:LP:AF:SS:ID   -0.0074:0.013:0.244125:0.869:119270:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0081:0.013:0.275724:0.87:119538:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0076:0.013:0.251812:0.87:119540:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869    ES:SE:LP:AF:SS:ID   -0.0072:0.013:0.236572:0.869:118906:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0091:0.013:0.309804:0.871:119185:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.102    ES:SE:LP:AF:SS:ID   0.012:0.018:0.29243:0.102:114987:rs10157329
1   761732  rs2286139   C   T   .   PASS    AF=0.863    ES:SE:LP:AF:SS:ID   -0.0095:0.013:0.337242:0.863:116334:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   -0.0076:0.013:0.251812:0.868:118131:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865    ES:SE:LP:AF:SS:ID   -0.0066:0.013:0.21467:0.865:116946:rs3115849
1   762632  rs3131948   T   A   .   PASS    AF=0.869    ES:SE:LP:AF:SS:ID   -0.0073:0.013:0.236572:0.869:117471:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0062:0.013:0.19382:0.129:119063:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.099    ES:SE:LP:AF:SS:ID   0.0031:0.019:0.0604807:0.099:113646:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.764    ES:SE:LP:AF:SS:ID   -0.016:0.0081:1.34679:0.764:119167:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105    ES:SE:LP:AF:SS:ID   0.0013:0.015:0.0268721:0.105:119688:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0067:0.013:0.21467:0.129:119061:rs59306077
1   769223  rs60320384  C   G   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0065:0.013:0.207608:0.129:119333:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.105    ES:SE:LP:AF:SS:ID   -0.00063:0.016:0.0132283:0.105:119405:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.104    ES:SE:LP:AF:SS:ID   0.0054:0.016:0.130768:0.104:118743:rs371458725
1   771823  rs2977605   T   C   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0064:0.013:0.207608:0.87:119269:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.005:0.013:0.154902:0.129:119266:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0067:0.013:0.21467:0.871:119244:rs2905039
1   774874  rs28810152  A   C   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0081:0.013:0.267606:0.87:118519:rs28810152
1   775181  rs61768182  A   G   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0076:0.013:0.251812:0.129:119274:rs61768182
1   775659  rs2905035   A   G   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0071:0.013:0.229148:0.87:119300:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0061:0.013:0.19382:0.871:119317:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.096    ES:SE:LP:AF:SS:ID   0.0052:0.018:0.107905:0.096:116781:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0049:0.013:0.148742:0.128:119423:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0054:0.013:0.167491:0.128:119688:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0061:0.013:0.19382:0.87:118775:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.095    ES:SE:LP:AF:SS:ID   -0.0016:0.02:0.0268721:0.095:113333:rs61768199
1   782981  rs6594026   C   T   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0042:0.013:0.124939:0.128:118966:rs6594026
1   783318  rs6686696   A   G   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.0053:0.013:0.161151:0.127:119380:rs6686696
1   785050  rs2905062   G   A   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0039:0.013:0.119186:0.87:118692:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0039:0.013:0.119186:0.87:118775:rs2980300
1   786995  rs61768202  G   A   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.0027:0.013:0.0757207:0.127:119260:rs61768202
1   787399  rs2905055   G   T   .   PASS    AF=0.863    ES:SE:LP:AF:SS:ID   -0.007:0.013:0.229148:0.863:113287:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.0086:0.014:0.283997:0.127:118012:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   -0.0065:0.013:0.207608:0.868:116098:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0089:0.013:0.29243:0.87:116958:rs2905053