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-1068,TotalVariants=2399832,VariantsNotRead=0,HarmonisedVariants=2399832,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-1068/ieu-a-1068_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T08:47:39.672443",
    "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-1068/ieu-a-1068.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1068/ieu-a-1068_data.vcf.gz; Date=Tue Feb  4 19:51:46 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-1068/ieu-a-1068.vcf.gz; Date=Sat May  9 15:36:02 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-1068/ieu-a-1068.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-1068/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 10:54:09 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1068/ieu-a-1068.vcf.gz ...
Read summary statistics for 2399832 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, 1141296 SNPs remain.
After merging with regression SNP LD, 1141296 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.1448 (0.1528)
Lambda GC: 0.9935
Mean Chi^2: 0.9859
Intercept: 0.994 (0.0067)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Wed Feb  5 10:54:38 2020
Total time elapsed: 28.59s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9207,
    "inflation_factor": 0.9926,
    "mean_EFFECT": -0.0001,
    "n": 2829,
    "n_snps": 2399832,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 20185,
    "n_est": 2745.5856,
    "ratio_se_n": 0.9851,
    "mean_diff": -0,
    "ratio_diff": 0.8268,
    "sd_y_est1": 1.0433,
    "sd_y_est2": 1.0278,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1141296,
    "ldsc_nsnp_merge_regression_ld": 1141296,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 0.994,
    "ldsc_intercept_se": 0.0067,
    "ldsc_lambda_gc": 0.9935,
    "ldsc_mean_chisq": 0.9859,
    "ldsc_ratio": 0.4255
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
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 1.000000 3 42 0 2399832 0 NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 8.595200e+00 5.662042e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA 7.877900e+07 5.567122e+07 1.1523e+04 3.263052e+07 7.015307e+07 1.142817e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA -1.348000e-04 4.781680e-02 -1.5430e+00 -2.480000e-02 -3.000000e-04 2.450000e-02 1.89500e+00 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA 4.166610e-02 2.423120e-02 2.6100e-02 2.870000e-02 3.350000e-02 4.490000e-02 1.01400e+00 ▇▁▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 5.017091e-01 2.874066e-01 3.7000e-06 2.542003e-01 5.016005e-01 7.503001e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 5.017096e-01 2.874080e-01 3.8000e-06 2.541664e-01 5.015999e-01 7.503470e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.000000 NA NA NA NA NA 3.633252e-01 2.711900e-01 1.0060e-02 1.285000e-01 2.999000e-01 5.624000e-01 9.89940e-01 ▇▅▃▃▂
numeric AF_reference 20185 0.991589 NA NA NA NA NA 3.650565e-01 2.532621e-01 1.9970e-04 1.523560e-01 3.051120e-01 5.485220e-01 1.00000e+00 ▇▆▅▃▂
numeric N 0 1.000000 NA NA NA NA NA 2.829000e+03 0.000000e+00 2.8290e+03 2.829000e+03 2.829000e+03 2.829000e+03 2.82900e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.2133 0.1193 0.0737904 0.0737874 0.03048 0.0371406 2829
1 723819 rs11804171 T A -0.2145 0.1185 0.0702797 0.0702762 0.03048 0.1345850 2829
1 723891 rs2977670 G C 0.2147 0.1170 0.0664492 0.0664994 0.96924 0.7799520 2829
1 750235 rs12138618 G A -0.2842 0.0837 0.0006870 0.0006851 0.08166 NA 2829
1 752566 rs3094315 G A 0.0261 0.1159 0.8217999 0.8218283 0.79180 0.7182510 2829
1 754192 rs3131968 A G -0.0237 0.1204 0.8438000 0.8439497 0.81280 0.6785140 2829
1 768448 rs12562034 G A -0.1445 0.0645 0.0250501 0.0250708 0.11050 0.1918930 2829
1 775659 rs2905035 A G -0.1157 0.0591 0.0501003 0.0502654 0.81280 0.7450080 2829
1 777122 rs2980319 A T -0.1173 0.0591 0.0472096 0.0471699 0.81280 0.7472040 2829
1 779322 rs4040617 A G 0.1173 0.0591 0.0472096 0.0471699 0.18720 0.2264380 2829
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51212875 rs2238837 A C 0.0339 0.0425 0.4246000 0.4250753 0.40970 0.3724040 2829
22 51216564 rs9616970 T C -0.0223 0.0458 0.6256004 0.6263295 0.13400 0.1563500 2829
22 51217134 rs117417021 A G 0.0176 0.0423 0.6771003 0.6773546 0.48450 0.2671730 2829
22 51222100 rs114553188 G T -0.1197 0.0628 0.0565900 0.0566436 0.07936 0.0880591 2829
22 51223637 rs375798137 G A -0.1197 0.0628 0.0565900 0.0566436 0.07936 0.0788738 2829
22 51229805 rs9616985 T C 0.0682 0.0609 0.2630002 0.2627697 0.05405 0.0730831 2829
23 35921591 rs2204667 C G 0.0267 0.0357 0.4543003 0.4545210 0.15410 NA 2829
23 51666786 rs14115 A G 0.0100 0.0688 0.8840001 0.8844355 0.06200 NA 2829
23 70163799 rs1626496 A C -0.0575 0.0519 0.2681001 0.2679051 0.03939 NA 2829
23 118495837 rs12882977 G A -0.0103 0.0273 0.7066006 0.7059586 0.42180 0.2307280 2829

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.03048  ES:SE:LP:AF:SS:ID   -0.2133:0.1193:1.132:0.03048:2829:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.03048  ES:SE:LP:AF:SS:ID   -0.2145:0.1185:1.15317:0.03048:2829:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.96924  ES:SE:LP:AF:SS:ID   0.2147:0.117:1.17751:0.96924:2829:rs2977670
1   750235  rs12138618  G   A   .   PASS    AF=0.08166  ES:SE:LP:AF:SS:ID   -0.2842:0.0837:3.16304:0.08166:2829:rs12138618
1   752566  rs3094315   G   A   .   PASS    AF=0.7918   ES:SE:LP:AF:SS:ID   0.0261:0.1159:0.0852339:0.7918:2829:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.8128   ES:SE:LP:AF:SS:ID   -0.0237:0.1204:0.0737605:0.8128:2829:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.1105   ES:SE:LP:AF:SS:ID   -0.1445:0.0645:1.60119:0.1105:2829:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.8128   ES:SE:LP:AF:SS:ID   -0.1157:0.0591:1.30016:0.8128:2829:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.8128   ES:SE:LP:AF:SS:ID   -0.1173:0.0591:1.32597:0.8128:2829:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.1872   ES:SE:LP:AF:SS:ID   0.1173:0.0591:1.32597:0.1872:2829:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8128   ES:SE:LP:AF:SS:ID   -0.1173:0.0591:1.32597:0.8128:2829:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.8131   ES:SE:LP:AF:SS:ID   -0.1173:0.0591:1.32597:0.8131:2829:rs2905062
1   798026  rs4951864   C   T   .   PASS    AF=0.8899   ES:SE:LP:AF:SS:ID   0.1799:0.0675:2.11357:0.8899:2829:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1104   ES:SE:LP:AF:SS:ID   -0.1846:0.0672:2.21961:0.1104:2829:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.2142   ES:SE:LP:AF:SS:ID   -0.0325:0.0557:0.2522:0.2142:2829:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.4612   ES:SE:LP:AF:SS:ID   0.0839:0.05:1.0284:0.4612:2829:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.2895   ES:SE:LP:AF:SS:ID   0.1155:0.0492:1.72561:0.2895:2829:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.2294   ES:SE:LP:AF:SS:ID   -0.0428:0.039:0.564952:0.2294:2829:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7401   ES:SE:LP:AF:SS:ID   -0.0248:0.0306:0.378824:0.7401:2829:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.2293   ES:SE:LP:AF:SS:ID   -0.0387:0.0392:0.491066:0.2293:2829:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5155   ES:SE:LP:AF:SS:ID   -0.0603:0.0395:0.895513:0.5155:2829:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5106   ES:SE:LP:AF:SS:ID   -0.0597:0.0391:0.898253:0.5106:2829:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.2174   ES:SE:LP:AF:SS:ID   -0.0395:0.0414:0.468266:0.2174:2829:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5106   ES:SE:LP:AF:SS:ID   -0.0099:0.0283:0.138585:0.5106:2829:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5104   ES:SE:LP:AF:SS:ID   -0.0099:0.0283:0.138585:0.5104:2829:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.2168   ES:SE:LP:AF:SS:ID   -0.022:0.0413:0.225848:0.2168:2829:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7174   ES:SE:LP:AF:SS:ID   -0.0142:0.0303:0.194635:0.7174:2829:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.2168   ES:SE:LP:AF:SS:ID   -0.022:0.0413:0.225848:0.2168:2829:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7424   ES:SE:LP:AF:SS:ID   -0.0132:0.0304:0.178421:0.7424:2829:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.4994   ES:SE:LP:AF:SS:ID   -0.0014:0.0279:0.0183626:0.4994:2829:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.98189  ES:SE:LP:AF:SS:ID   -0.1261:0.1473:0.406714:0.98189:2829:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.6052   ES:SE:LP:AF:SS:ID   0.0303:0.0282:0.547753:0.6052:2829:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1886   ES:SE:LP:AF:SS:ID   -0.0417:0.0375:0.575118:0.1886:2829:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1857   ES:SE:LP:AF:SS:ID   -0.0417:0.0375:0.575118:0.1857:2829:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.7296   ES:SE:LP:AF:SS:ID   0.012:0.031:0.15602:0.7296:2829:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.0529   ES:SE:LP:AF:SS:ID   -0.0545:0.0453:0.640544:0.0529:2829:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.09919  ES:SE:LP:AF:SS:ID   -0.055:0.0402:0.765483:0.09919:2829:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.09919  ES:SE:LP:AF:SS:ID   -0.0586:0.0402:0.838333:0.09919:2829:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05322  ES:SE:LP:AF:SS:ID   -0.0527:0.0446:0.623606:0.05322:2829:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1112   ES:SE:LP:AF:SS:ID   -0.0517:0.0397:0.713993:0.1112:2829:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.06613  ES:SE:LP:AF:SS:ID   -0.0495:0.0443:0.579055:0.06613:2829:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3258   ES:SE:LP:AF:SS:ID   -0.0009:0.0297:0.0103722:0.3258:2829:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.04543  ES:SE:LP:AF:SS:ID   -0.0511:0.0832:0.268492:0.04543:2829:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.06642  ES:SE:LP:AF:SS:ID   -0.0391:0.0443:0.423889:0.06642:2829:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.06642  ES:SE:LP:AF:SS:ID   -0.0384:0.0449:0.405718:0.06642:2829:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.06642  ES:SE:LP:AF:SS:ID   -0.0424:0.0449:0.461678:0.06642:2829:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.3921   ES:SE:LP:AF:SS:ID   -0.0194:0.0283:0.307417:0.3921:2829:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.04457  ES:SE:LP:AF:SS:ID   -0.0412:0.0849:0.202594:0.04457:2829:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5233   ES:SE:LP:AF:SS:ID   0.0323:0.0281:0.600499:0.5233:2829:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7884   ES:SE:LP:AF:SS:ID   0.0331:0.0349:0.465086:0.7884:2829:rs6682475