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-837,TotalVariants=2307473,VariantsNotRead=0,HarmonisedVariants=2307473,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-837/ieu-a-837_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T08:39:05.594328",
    "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-837/ieu-a-837.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-837/ieu-a-837_data.vcf.gz; Date=Tue Feb  4 09:02:40 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-837/ieu-a-837.vcf.gz; Date=Sat May  9 20:53:02 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-837/ieu-a-837.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-837/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 19:25:20 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-837/ieu-a-837.vcf.gz ...
Read summary statistics for 2307473 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, 1108496 SNPs remain.
After merging with regression SNP LD, 1108496 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0941 (0.0065)
Lambda GC: 1.2365
Mean Chi^2: 1.2759
Intercept: 1.0385 (0.009)
Ratio: 0.1393 (0.0327)
Analysis finished at Tue Feb  4 19:25:48 2020
Total time elapsed: 28.46s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9096,
    "inflation_factor": 1.2074,
    "mean_EFFECT": 0,
    "n": 126559,
    "n_snps": 2307473,
    "n_clumped_hits": 4,
    "n_p_sig": 11,
    "n_mono": 0,
    "n_ns": 0,
    "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": 18060,
    "n_est": 104063.0261,
    "ratio_se_n": 0.9068,
    "mean_diff": -7.2951e-06,
    "ratio_diff": 0.8291,
    "sd_y_est1": 1.0421,
    "sd_y_est2": 0.9449,
    "r2_sum1": 0.001,
    "r2_sum2": 0.0009,
    "r2_sum3": 0.0011,
    "r2_sum4": 0.001,
    "ldsc_nsnp_merge_refpanel_ld": 1108496,
    "ldsc_nsnp_merge_regression_ld": 1108496,
    "ldsc_observed_scale_h2_beta": 0.0941,
    "ldsc_observed_scale_h2_se": 0.0065,
    "ldsc_intercept_beta": 1.0385,
    "ldsc_intercept_se": 0.009,
    "ldsc_lambda_gc": 1.2365,
    "ldsc_mean_chisq": 1.2759,
    "ldsc_ratio": 0.1395
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
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 42 0 2307473 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 8.561442e+00 5.643161e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.889051e+07 5.556291e+07 1.61110e+04 3.281803e+07 7.034670e+07 1.142963e+08 2.492107e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.580000e-05 5.564400e-03 -3.40000e-02 -4.000000e-03 0.000000e+00 4.000000e-03 3.500000e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 4.915900e-03 1.039100e-03 4.00000e-03 4.000000e-03 5.000000e-03 6.000000e-03 1.500000e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.696646e-01 2.965536e-01 0.00000e+00 2.061000e-01 4.585999e-01 7.261996e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.674438e-01 3.017298e-01 0.00000e+00 2.112995e-01 4.532547e-01 7.388827e-01 1.000000e+00 ▇▆▆▆▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.678334e-01 2.687034e-01 1.00000e-02 1.300000e-01 3.100000e-01 5.700000e-01 9.900000e-01 ▇▆▃▃▂
numeric AF_reference 18060 0.9921733 NA NA NA NA NA 3.702108e-01 2.500943e-01 1.99700e-04 1.599440e-01 3.128990e-01 5.523160e-01 1.000000e+00 ▇▇▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.265590e+05 0.000000e+00 1.26559e+05 1.265590e+05 1.265590e+05 1.265590e+05 1.265590e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 1003629 rs4075116 C T 0.001 0.005 0.8374001 0.8414806 0.78 0.720647 126559
1 1005806 rs3934834 C T -0.007 0.005 0.1762999 0.1615133 0.13 0.223442 126559
1 1017170 rs3766193 C G 0.006 0.004 0.1370999 0.1336144 0.60 0.575479 126559
1 1017197 rs3766192 C T 0.007 0.004 0.0978003 0.0801183 0.61 0.511182 126559
1 1017587 rs3766191 C T -0.008 0.005 0.1330001 0.1095986 0.11 0.171126 126559
1 1018562 rs9442371 C T 0.006 0.004 0.1567000 0.1336144 0.62 0.530152 126559
1 1018704 rs9442372 A G 0.005 0.004 0.2272998 0.2112995 0.63 0.611022 126559
1 1021346 rs10907177 A G -0.008 0.005 0.1198001 0.1095986 0.13 0.178914 126559
1 1021415 rs3737728 A G 0.003 0.004 0.4356001 0.4532547 0.74 0.812700 126559
1 1021583 rs10907178 A C -0.008 0.005 0.1201999 0.1095986 0.11 0.173722 126559
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51163138 rs715586 C T 0.000 0.005 0.9653000 1.0000000 0.16 0.0902556 126559
22 51165664 rs8137951 G A -0.003 0.004 0.5153995 0.4532547 0.26 0.4063500 126559
22 51171497 rs2301584 G A -0.006 0.005 0.2775000 0.2301393 0.14 0.2533950 126559
22 51175626 rs3810648 A G -0.008 0.007 0.1997998 0.2530979 0.07 0.1084270 126559
22 51178090 rs2285395 G A -0.009 0.007 0.1912000 0.1985428 0.07 0.0666933 126559
22 51196164 rs8136603 A T -0.010 0.007 0.1457002 0.1531275 0.07 0.1427720 126559
23 35921591 rs2204667 C G 0.002 0.005 0.7413000 0.6891565 0.16 NA 126559
23 51666786 rs14115 A G -0.016 0.007 0.0140501 0.0222710 0.03 NA 126559
23 70163799 rs1626496 A C -0.009 0.006 0.1265001 0.1336144 0.07 NA 126559
23 118495837 rs12882977 G A -0.002 0.004 0.5903003 0.6170751 0.49 0.2307280 126559

bcf preview

1   1003629 rs4075116   C   T   .   PASS    AF=0.78 ES:SE:LP:AF:SS:ID   0.001:0.005:0.077067:0.78:126559:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.13 ES:SE:LP:AF:SS:ID   -0.007:0.005:0.753748:0.13:126559:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   0.006:0.004:0.862963:0.6:126559:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.61 ES:SE:LP:AF:SS:ID   0.007:0.004:1.00966:0.61:126559:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   -0.008:0.005:0.876148:0.11:126559:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.62 ES:SE:LP:AF:SS:ID   0.006:0.004:0.804931:0.62:126559:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.63 ES:SE:LP:AF:SS:ID   0.005:0.004:0.643401:0.63:126559:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.13 ES:SE:LP:AF:SS:ID   -0.008:0.005:0.921543:0.13:126559:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.74 ES:SE:LP:AF:SS:ID   0.003:0.004:0.360912:0.74:126559:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   -0.008:0.005:0.920096:0.11:126559:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.76 ES:SE:LP:AF:SS:ID   0.003:0.004:0.353204:0.76:126559:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.59 ES:SE:LP:AF:SS:ID   0.007:0.004:1.06379:0.59:126559:rs6701114
1   1030565 rs6687776   C   T   .   PASS    AF=0.09 ES:SE:LP:AF:SS:ID   -0.01:0.005:1.1831:0.09:126559:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.09 ES:SE:LP:AF:SS:ID   -0.008:0.005:0.852324:0.09:126559:rs6678318
1   1036959 rs11579015  T   C   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.006:0.006:0.555799:0.06:126559:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   -0.007:0.005:0.63865:0.08:126559:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.07 ES:SE:LP:AF:SS:ID   -0.006:0.006:0.512014:0.07:126559:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.004:0.006:0.305395:0.06:126559:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.07 ES:SE:LP:AF:SS:ID   -0.005:0.006:0.45892:0.07:126559:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.004:0.006:0.315244:0.06:126559:rs4970409
1   1060608 rs17160824  G   A   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.004:0.006:0.284916:0.06:126559:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.004:0.006:0.328827:0.06:126559:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.004:0.006:0.294821:0.06:126559:rs12748370
1   1064979 rs2298217   C   T   .   PASS    AF=0.09 ES:SE:LP:AF:SS:ID   -0.007:0.005:0.646276:0.09:126559:rs2298217
1   1077064 rs4970357   C   A   .   PASS    AF=0.93 ES:SE:LP:AF:SS:ID   0.004:0.006:0.253599:0.93:126559:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.91 ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0379623:0.91:126559:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.97 ES:SE:LP:AF:SS:ID   0:0.007:0.0109508:0.97:126559:rs4970358
1   1097335 rs9442385   T   G   .   PASS    AF=0.94 ES:SE:LP:AF:SS:ID   -0.002:0.006:0.145148:0.94:126559:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.94 ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0393865:0.94:126559:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.96 ES:SE:LP:AF:SS:ID   0.001:0.007:0.0390063:0.96:126559:rs1891905
1   1121014 rs3813204   G   A   .   PASS    AF=0.13 ES:SE:LP:AF:SS:ID   0:0.006:0.0290026:0.13:126559:rs3813204
1   1121794 rs11260549  G   A   .   PASS    AF=0.13 ES:SE:LP:AF:SS:ID   -0.002:0.006:0.123551:0.13:126559:rs11260549
1   1124663 rs6684820   G   A   .   PASS    AF=0.28 ES:SE:LP:AF:SS:ID   0:0.005:0.0183173:0.28:126559:rs6684820
1   1125553 rs10907174  A   T   .   PASS    AF=0.24 ES:SE:LP:AF:SS:ID   -0.001:0.005:0.119186:0.24:126559:rs10907174
1   1129672 rs11260554  G   T   .   PASS    AF=0.13 ES:SE:LP:AF:SS:ID   0.001:0.006:0.0323116:0.13:126559:rs11260554
1   1130727 rs10907175  A   C   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0544822:0.11:126559:rs10907175
1   1135242 rs9729550   A   C   .   PASS    AF=0.29 ES:SE:LP:AF:SS:ID   0:0.005:0.032031:0.29:126559:rs9729550
1   1138913 rs3819001   T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   -0.003:0.007:0.16877:0.05:126559:rs3819001
1   1140435 rs1815606   G   T   .   PASS    AF=0.33 ES:SE:LP:AF:SS:ID   -0.001:0.005:0.0731947:0.33:126559:rs1815606
1   1143657 rs3753348   C   G   .   PASS    AF=0.03 ES:SE:LP:AF:SS:ID   -0.006:0.007:0.370183:0.03:126559:rs3753348
1   1151300 rs3813200   C   T   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   0.003:0.008:0.157391:0.02:126559:rs3813200
1   1152631 rs11721 C   A   .   PASS    AF=0.09 ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0886293:0.09:126559:rs11721
1   1156131 rs2887286   T   C   .   PASS    AF=0.19 ES:SE:LP:AF:SS:ID   0.006:0.005:0.553618:0.19:126559:rs2887286
1   1158277 rs3813199   G   A   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   0.003:0.006:0.251579:0.11:126559:rs3813199
1   1162435 rs3766186   C   A   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   0.004:0.006:0.322758:0.11:126559:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.002:0.005:0.184223:0.15:126559:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   -0.008:0.007:0.676335:0.05:126559:rs11260562
1   1176597 rs6675798   T   C   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   0.004:0.006:0.308388:0.11:126559:rs6675798
1   1181751 rs6603783   T   C   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   0.004:0.006:0.309538:0.11:126559:rs6603783
1   1188225 rs6603787   G   T   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.001:0.007:0.0475466:0.08:126559:rs6603787