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-32,TotalVariants=11094790,VariantsNotRead=0,HarmonisedVariants=11094790,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-32/ieu-a-32_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T11:45:40.934644",
    "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-32/ieu-a-32.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-32/ieu-a-32_data.vcf.gz; Date=Tue Feb  4 17:00:32 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-32/ieu-a-32.vcf.gz; Date=Sun May 10 14:20:00 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-32/ieu-a-32.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-32/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 08:51:23 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-32/ieu-a-32.vcf.gz ...
Read summary statistics for 11094790 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, 1289446 SNPs remain.
After merging with regression SNP LD, 1289446 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2573 (0.0289)
Lambda GC: 1.1264
Mean Chi^2: 1.1817
Intercept: 1.0452 (0.0079)
Ratio: 0.2488 (0.0435)
Analysis finished at Wed Feb  5 08:53:08 2020
Total time elapsed: 1.0m:44.95s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9547,
    "inflation_factor": 1.0757,
    "mean_EFFECT": 0.0003,
    "n": 27432,
    "n_snps": 11094790,
    "n_clumped_hits": 39,
    "n_p_sig": 6616,
    "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": 339482,
    "n_est": 26508.4969,
    "ratio_se_n": 0.983,
    "mean_diff": 0.0011,
    "ratio_diff": 0.8472,
    "sd_y_est1": 2.6128,
    "sd_y_est2": 2.5685,
    "r2_sum1": 0.6157,
    "r2_sum2": 0.0902,
    "r2_sum3": 0.0933,
    "r2_sum4": 0.0898,
    "ldsc_nsnp_merge_refpanel_ld": 1289446,
    "ldsc_nsnp_merge_regression_ld": 1289446,
    "ldsc_observed_scale_h2_beta": 0.2573,
    "ldsc_observed_scale_h2_se": 0.0289,
    "ldsc_intercept_beta": 1.0452,
    "ldsc_intercept_se": 0.0079,
    "ldsc_lambda_gc": 1.1264,
    "ldsc_mean_chisq": 1.1817,
    "ldsc_ratio": 0.2488
}

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 TRUE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio FALSE
ldsc_intercept_beta FALSE
n_clumped_hits FALSE
r2_sum1 TRUE
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 59 0 11094788 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 8.677141e+00 5.778864e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.868287e+07 5.643491e+07 8.28000e+02 3.243807e+07 6.919840e+07 1.144908e+08 2.492395e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 3.268000e-04 7.859701e-01 -7.01648e+02 -3.280220e-02 1.498900e-03 3.759800e-02 6.374370e+02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.946383e-01 2.808485e+01 2.05000e-02 2.600000e-02 4.720000e-02 1.238000e-01 3.297000e+04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.883115e-01 2.921557e-01 0.00000e+00 2.322999e-01 4.842002e-01 7.414997e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.883110e-01 2.921562e-01 0.00000e+00 2.322635e-01 4.842455e-01 7.414965e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.954149e-01 2.549758e-01 1.75270e-03 1.100000e-02 6.620480e-02 2.984600e-01 9.979250e-01 ▇▂▁▁▁
numeric AF_reference 339482 0.9694017 NA NA NA NA NA 2.001557e-01 2.492539e-01 0.00000e+00 1.038340e-02 8.746010e-02 3.075080e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 2.743200e+04 0.000000e+00 2.74320e+04 2.743200e+04 2.743200e+04 2.743200e+04 2.743200e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10611 rs189107123 C G 0.0591981 0.1443 0.6818000 0.6816275 0.0180000 NA 27432
1 51479 rs116400033 T A -0.0701006 0.0479 0.1432000 0.1433366 0.1972380 0.1281950 27432
1 52058 rs62637813 G C 0.0558036 0.0934 0.5505997 0.5501943 0.0433032 NA 27432
1 52144 rs190291950 T A -0.0306035 0.1730 0.8595000 0.8595878 0.0118476 0.0009984 27432
1 54421 rs146477069 A G -0.0959009 0.0879 0.2754000 0.2752629 0.0574920 NA 27432
1 54490 rs141149254 G A -0.0878044 0.0531 0.0981997 0.0982156 0.1492380 0.0960463 27432
1 54676 rs2462492 C T 0.0021976 0.0505 0.9656001 0.9652899 0.1697620 NA 27432
1 54753 rs143174675 T G -0.1884030 0.1145 0.0999402 0.0998789 0.0307460 NA 27432
1 55164 rs3091274 C A 0.0465018 0.0872 0.5936001 0.5938415 0.9495080 0.9233230 27432
1 55299 rs10399749 C T 0.0392976 0.0511 0.4419000 0.4418736 0.1692540 NA 27432
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51229855 rs144549712 G A 0.0414010 0.0547 0.4497995 0.4491254 0.0913273 0.1160140 27432
22 51234159 rs8138356 T A 0.2742020 0.3678 0.4560002 0.4559578 0.0068865 0.0215655 27432
22 51234199 rs6010092 T C 0.6420930 0.6050 0.2885998 0.2885487 0.0052540 0.0313498 27432
22 51234677 rs189571549 A C 0.5086950 0.2639 0.0538605 0.0539043 0.0062540 0.0227636 27432
22 51234799 rs191117135 G A 0.5949000 0.1894 0.0016810 0.0016839 0.0083345 0.0059904 27432
22 51237063 rs3896457 T C 0.0058974 0.0313 0.8506999 0.8505521 0.2682700 0.2050720 27432
22 51238249 rs149733995 A C 0.0819044 0.0593 0.1673998 0.1672214 0.0694920 NA 27432
23 50040891 rs192267219 C T -0.2475000 0.1458 0.0896603 0.0895963 0.9867460 0.0222517 27432
23 51866774 rs150899468 C A 0.5898010 0.5295 0.2652998 0.2653294 0.9945080 0.9965560 27432
23 100784211 rs188350543 C A -0.0158957 0.0265 0.5497003 0.5486144 0.7390000 0.6498010 27432

bcf preview

1   10611   rs189107123 C   G   .   PASS    AF=0.018    ES:SE:LP:AF:SS:ID   0.0591981:0.1443:0.166343:0.018:27432:rs189107123
1   51479   rs116400033 T   A   .   PASS    AF=0.197238 ES:SE:LP:AF:SS:ID   -0.0701006:0.0479:0.844057:0.197238:27432:rs116400033
1   52058   rs62637813  G   C   .   PASS    AF=0.0433032    ES:SE:LP:AF:SS:ID   0.0558036:0.0934:0.259164:0.0433032:27432:rs62637813
1   52144   rs190291950 T   A   .   PASS    AF=0.0118476    ES:SE:LP:AF:SS:ID   -0.0306035:0.173:0.0657541:0.0118476:27432:rs190291950
1   54421   rs146477069 A   G   .   PASS    AF=0.057492 ES:SE:LP:AF:SS:ID   -0.0959009:0.0879:0.560036:0.057492:27432:rs146477069
1   54490   rs141149254 G   A   .   PASS    AF=0.149238 ES:SE:LP:AF:SS:ID   -0.0878044:0.0531:1.00789:0.149238:27432:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.169762 ES:SE:LP:AF:SS:ID   0.00219758:0.0505:0.0152027:0.169762:27432:rs2462492
1   54753   rs143174675 T   G   .   PASS    AF=0.030746 ES:SE:LP:AF:SS:ID   -0.188403:0.1145:1.00026:0.030746:27432:rs143174675
1   55164   rs3091274   C   A   .   PASS    AF=0.949508 ES:SE:LP:AF:SS:ID   0.0465018:0.0872:0.226506:0.949508:27432:rs3091274
1   55299   rs10399749  C   T   .   PASS    AF=0.169254 ES:SE:LP:AF:SS:ID   0.0392976:0.0511:0.354676:0.169254:27432:rs10399749
1   55326   rs3107975   T   C   .   PASS    AF=0.021    ES:SE:LP:AF:SS:ID   0.0322959:0.125:0.0991415:0.021:27432:rs3107975
1   55394   rs2949420   T   A   .   PASS    AF=0.013073 ES:SE:LP:AF:SS:ID   -0.00879859:0.1588:0.0195875:0.013073:27432:rs2949420
1   55850   rs191890754 C   G   .   PASS    AF=0.007254 ES:SE:LP:AF:SS:ID   -0.0379025:0.331:0.0415795:0.007254:27432:rs191890754
1   55852   rs184233019 G   C   .   PASS    AF=0.00575904   ES:SE:LP:AF:SS:ID   0.0724044:0.5699:0.0462886:0.00575904:27432:rs184233019
1   58814   rs114420996 G   A   .   PASS    AF=0.0838922    ES:SE:LP:AF:SS:ID   0.158703:0.0679:1.71265:0.0838922:27432:rs114420996
1   61462   rs56992750  T   A   .   PASS    AF=0.00716893   ES:SE:LP:AF:SS:ID   0.391299:0.2719:0.823619:0.00716893:27432:rs56992750
1   61987   rs76735897  A   G   .   PASS    AF=0.340762 ES:SE:LP:AF:SS:ID   -0.0165031:0.0403:0.166025:0.340762:27432:rs76735897
1   61989   rs77573425  G   C   .   PASS    AF=0.340762 ES:SE:LP:AF:SS:ID   -0.0162005:0.0403:0.163106:0.340762:27432:rs77573425
1   64649   rs181431124 A   C   .   PASS    AF=0.019254 ES:SE:LP:AF:SS:ID   0.2589:0.1323:1.29783:0.019254:27432:rs181431124
1   66162   rs62639105  A   T   .   PASS    AF=0.331762 ES:SE:LP:AF:SS:ID   -0.0179971:0.0404:0.18356:0.331762:27432:rs62639105
1   66176   rs28552463  T   A   .   PASS    AF=0.00801289   ES:SE:LP:AF:SS:ID   0.517299:0.2272:1.64207:0.00801289:27432:rs28552463
1   66219   rs181028663 A   T   .   PASS    AF=0.017746 ES:SE:LP:AF:SS:ID   -0.0495994:0.1565:0.124187:0.017746:27432:rs181028663
1   66331   rs186063952 A   C   .   PASS    AF=0.006254 ES:SE:LP:AF:SS:ID   0.503999:0.3196:0.940058:0.006254:27432:rs186063952
1   66442   rs192044252 T   A   .   PASS    AF=0.0188238    ES:SE:LP:AF:SS:ID   0.0207042:0.1515:0.0500736:0.0188238:27432:rs192044252
1   66457   rs13328655  T   A   .   PASS    AF=0.0108778    ES:SE:LP:AF:SS:ID   0.0531047:0.1868:0.10997:0.0108778:27432:rs13328655
1   66507   rs12401368  T   A   .   PASS    AF=0.100433 ES:SE:LP:AF:SS:ID   0.0803996:0.0625:0.70224:0.100433:27432:rs12401368
1   73841   rs143773730 C   T   .   PASS    AF=0.231254 ES:SE:LP:AF:SS:ID   -0.0135007:0.0452:0.116509:0.231254:27432:rs143773730
1   77961   rs78385339  G   A   .   PASS    AF=0.0584062    ES:SE:LP:AF:SS:ID   -0.1359:0.0881:0.909037:0.0584062:27432:rs78385339
1   79137   rs143777184 A   T   .   PASS    AF=0.006    ES:SE:LP:AF:SS:ID   -0.592597:0.5094:0.611366:0.006:27432:rs143777184
1   79772   rs147215883 C   G   .   PASS    AF=0.081    ES:SE:LP:AF:SS:ID   -0.0820039:0.0735:0.57741:0.081:27432:rs147215883
1   82163   rs139113303 G   A   .   PASS    AF=0.0553746    ES:SE:LP:AF:SS:ID   0.018596:0.0862:0.0815503:0.0553746:27432:rs139113303
1   82249   rs1851945   A   G   .   PASS    AF=0.034746 ES:SE:LP:AF:SS:ID   -0.0489997:0.1172:0.170118:0.034746:27432:rs1851945
1   82609   rs149189449 C   G   .   PASS    AF=0.059    ES:SE:LP:AF:SS:ID   0.046201:0.0839:0.235376:0.059:27432:rs149189449
1   82676   rs185237834 T   G   .   PASS    AF=0.088    ES:SE:LP:AF:SS:ID   -0.0128965:0.0696:0.0692547:0.088:27432:rs185237834
1   82734   rs4030331   T   C   .   PASS    AF=0.180492 ES:SE:LP:AF:SS:ID   0.0193969:0.052:0.148803:0.180492:27432:rs4030331
1   84002   rs28850140  G   A   .   PASS    AF=0.103746 ES:SE:LP:AF:SS:ID   0.0108015:0.064:0.0628333:0.103746:27432:rs28850140
1   84010   rs186443818 G   A   .   PASS    AF=0.0544048    ES:SE:LP:AF:SS:ID   0.0493995:0.0849:0.25096:0.0544048:27432:rs186443818
1   84139   rs183605470 A   T   .   PASS    AF=0.01 ES:SE:LP:AF:SS:ID   -0.091804:0.2303:0.161088:0.01:27432:rs183605470
1   84244   rs191297051 A   C   .   PASS    AF=0.100746 ES:SE:LP:AF:SS:ID   -0.0841021:0.067:0.677988:0.100746:27432:rs191297051
1   84295   rs183209871 G   A   .   PASS    AF=0.00606575   ES:SE:LP:AF:SS:ID   0.181104:0.3653:0.207538:0.00606575:27432:rs183209871
1   85063   rs187802690 T   C   .   PASS    AF=0.024746 ES:SE:LP:AF:SS:ID   -0.0352996:0.1273:0.107071:0.024746:27432:rs187802690
1   85597   rs192472955 A   C   .   PASS    AF=0.078254 ES:SE:LP:AF:SS:ID   -0.0736965:0.0731:0.504178:0.078254:27432:rs192472955
1   86018   rs142878000 C   G   .   PASS    AF=0.102    ES:SE:LP:AF:SS:ID   -0.0503033:0.0659:0.35125:0.102:27432:rs142878000
1   86028   rs114608975 T   C   .   PASS    AF=0.060746 ES:SE:LP:AF:SS:ID   -0.0301023:0.0836:0.143211:0.060746:27432:rs114608975
1   86065   rs116504101 G   C   .   PASS    AF=0.0634254    ES:SE:LP:AF:SS:ID   0.0178989:0.081:0.0834408:0.0634254:27432:rs116504101
1   86303   rs2949417   G   T   .   PASS    AF=0.102254 ES:SE:LP:AF:SS:ID   -0.0577986:0.0648:0.428524:0.102254:27432:rs2949417
1   86331   rs115209712 A   G   .   PASS    AF=0.104254 ES:SE:LP:AF:SS:ID   -0.0589008:0.0637:0.449283:0.104254:27432:rs115209712
1   87021   rs188486692 T   C   .   PASS    AF=0.014    ES:SE:LP:AF:SS:ID   -0.225597:0.16:0.799697:0.014:27432:rs188486692
1   87190   rs1524602   G   A   .   PASS    AF=0.151238 ES:SE:LP:AF:SS:ID   -0.0335051:0.0564:0.257746:0.151238:27432:rs1524602
1   87409   rs139490478 C   T   .   PASS    AF=0.0631762    ES:SE:LP:AF:SS:ID   0.0287041:0.0808:0.141222:0.0631762:27432:rs139490478