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-94,TotalVariants=2735337,VariantsNotRead=0,HarmonisedVariants=2735337,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-94/ieu-a-94_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T08:55:47.112574",
    "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-94/ieu-a-94.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-94/ieu-a-94_data.vcf.gz; Date=Tue Feb  4 19:14:52 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-94/ieu-a-94.vcf.gz; Date=Sat May  9 18:06:17 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-94/ieu-a-94.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-94/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 10:59:06 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-94/ieu-a-94.vcf.gz ...
Read summary statistics for 2735337 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, 1272364 SNPs remain.
After merging with regression SNP LD, 1272364 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1626 (0.01)
Lambda GC: 1.0047
Mean Chi^2: 1.0362
Intercept: 0.869 (0.0051)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 10:59:38 2020
Total time elapsed: 32.38s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9172,
    "inflation_factor": 1,
    "mean_EFFECT": 0.0001,
    "n": 58665.1,
    "n_snps": 2735337,
    "n_clumped_hits": 10,
    "n_p_sig": 356,
    "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": 475806,
    "n_miss_AF_reference": 27039,
    "n_est": 57201.1188,
    "ratio_se_n": 0.9874,
    "mean_diff": -0,
    "ratio_diff": 4.0749,
    "sd_y_est1": 1.1128,
    "sd_y_est2": 1.0988,
    "r2_sum1": 0.0093,
    "r2_sum2": 0.0075,
    "r2_sum3": 0.0077,
    "r2_sum4": 0.0081,
    "ldsc_nsnp_merge_refpanel_ld": 1272364,
    "ldsc_nsnp_merge_regression_ld": 1272364,
    "ldsc_observed_scale_h2_beta": 0.1626,
    "ldsc_observed_scale_h2_se": 0.01,
    "ldsc_intercept_beta": 0.869,
    "ldsc_intercept_se": 0.0051,
    "ldsc_lambda_gc": 1.0047,
    "ldsc_mean_chisq": 1.0362,
    "ldsc_ratio": -3.6188
}

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 42 0 2735337 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 8.614609e+00 5.688515e+00 1.0000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.881189e+07 5.589827e+07 6689.0000 3.245666e+07 6.999861e+07 1.144279e+08 2.492114e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.492000e-04 1.647549e-01 -260.0000 -6.600000e-03 0.000000e+00 6.800000e-03 3.200000e+01 ▁▁▁▁▇
numeric SE 0 1.0000000 NA NA NA NA NA 1.944840e-02 7.781500e-02 0.0062 6.900000e-03 8.400000e-03 1.300000e-02 1.000000e+02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.985740e-01 2.897486e-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 4.987640e-01 2.896342e-01 0.0000 2.475789e-01 4.996758e-01 7.498474e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 475806 0.8260521 NA NA NA NA NA 3.565755e-01 2.754929e-01 0.0083 1.167000e-01 2.917000e-01 5.583000e-01 9.917000e-01 ▇▅▃▂▂
numeric AF_reference 27039 0.9901149 NA NA NA NA NA 3.543675e-01 2.611583e-01 0.0000 1.343850e-01 2.889380e-01 5.409350e-01 1.000000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 5.224462e+04 1.549762e+04 113.0000 5.699510e+04 5.860350e+04 5.861700e+04 5.866510e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 564477 rs6650104 A G 0.1300 0.130 0.3300000 0.3173105 NA 0.0003994 1699.56
1 721290 rs12565286 G C 0.0200 0.028 0.4700002 0.4750505 NA 0.0371406 21734.00
1 723819 rs11804171 T A 0.0200 0.028 0.4799997 0.4750505 NA 0.1345850 21749.00
1 723891 rs2977670 G C 0.0069 0.039 0.8600001 0.8595688 NA 0.7799520 11159.00
1 752566 rs3094315 G A 0.0007 0.011 0.9500000 0.9492598 NA 0.7182510 36556.80
1 752721 rs3131972 A G 0.0570 0.048 0.2399999 0.2350305 NA 0.6533550 1699.75
1 753541 rs2073813 G A -0.0055 0.015 0.7199992 0.7138677 NA 0.3019170 23271.00
1 754182 rs3131969 A G 0.0640 0.051 0.2099999 0.2095144 NA 0.6785140 1699.92
1 754192 rs3131968 A G -0.0130 0.019 0.5099998 0.4938422 NA 0.6785140 14540.10
1 760912 rs1048488 C T 0.0600 0.049 0.2200002 0.2207675 NA 0.7340260 1699.94
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51212875 rs2238837 A C 0.0050 0.0120 0.6800001 0.6769222 0.3917 0.3724040 28617.90
22 51213613 rs34726907 C T -0.0260 0.0510 0.6100002 0.6101888 NA 0.1727240 1873.00
22 51219006 rs28729663 G A -0.0580 0.0460 0.2099999 0.2073558 NA 0.2052720 2004.00
22 51229805 rs9616985 T C 0.0100 0.0220 0.6499995 0.6494363 0.0917 0.0730831 27397.00
23 35921591 rs2204667 C G -0.0089 0.0086 0.2999998 0.3007232 0.1667 NA 58614.00
23 51666786 rs14115 A G -0.0018 0.0140 0.9000000 0.8976968 0.0250 NA 58470.40
23 70163799 rs1626496 A C -0.0300 0.0120 0.0140001 0.0124193 0.0750 NA 58619.30
23 91415872 rs6562597 G A -0.0050 0.0230 0.8300000 0.8279034 0.0083 0.0021192 56688.80
23 117417363 rs11541996 G A 0.0330 0.2500 0.9000000 0.8949843 NA NA 1699.87
23 118495837 rs12882977 G A 0.0045 0.0064 0.4799997 0.4819779 0.5167 0.2307280 58615.60

bcf preview

1   564477  rs6650104   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.13:0.13:0.481486:1699.56:rs6650104
1   721290  rs12565286  G   C   .   PASS    .   ES:SE:LP:SS:ID  0.02:0.028:0.327902:21734:rs12565286
1   723819  rs11804171  T   A   .   PASS    .   ES:SE:LP:SS:ID  0.02:0.028:0.318759:21749:rs11804171
1   723891  rs2977670   G   C   .   PASS    .   ES:SE:LP:SS:ID  0.0069:0.039:0.0655015:11159:rs2977670
1   752566  rs3094315   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0007:0.011:0.0222764:36556.8:rs3094315
1   752721  rs3131972   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.057:0.048:0.619789:1699.75:rs3131972
1   753541  rs2073813   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0055:0.015:0.142668:23271:rs2073813
1   754182  rs3131969   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.064:0.051:0.677781:1699.92:rs3131969
1   754192  rs3131968   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.013:0.019:0.29243:14540.1:rs3131968
1   760912  rs1048488   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.06:0.049:0.657577:1699.94:rs1048488
1   761732  rs2286139   C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.01:0.038:0.102373:2872:rs2286139
1   768448  rs12562034  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.023:0.022:0.537602:19505.3:rs12562034
1   775659  rs2905035   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.0004:0.012:0.0132283:37810.1:rs2905035
1   776546  rs12124819  A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0074:0.023:0.130768:6478.11:rs12124819
1   777122  rs2980319   A   T   .   PASS    .   ES:SE:LP:SS:ID  -0.0007:0.012:0.0222764:37808.9:rs2980319
1   779322  rs4040617   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0008:0.012:0.0222764:37741.5:rs4040617
1   780785  rs2977612   T   A   .   PASS    .   ES:SE:LP:SS:ID  0.0008:0.012:0.0222764:37809.8:rs2977612
1   784023  rs17160939  A   G   .   PASS    .   ES:SE:LP:SS:ID  0.038:0.072:0.221849:5677.22:rs17160939
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.001:0.012:0.0315171:37809.7:rs2905062
1   785989  rs2980300   T   C   .   PASS    .   ES:SE:LP:SS:ID  0.004:0.012:0.136677:37750.7:rs2980300
1   798026  rs4951864   C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.026:0.023:0.60206:19376.4:rs4951864
1   798801  rs12132517  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.032:0.023:0.769551:19375.5:rs12132517
1   798959  rs11240777  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.015:0.015:0.522879:21780.7:rs11240777
1   838555  rs4970383   C   A   .   PASS    .   ES:SE:LP:SS:ID  0.014:0.042:0.136677:1699.99:rs4970383
1   846808  rs4475691   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.033:0.028:0.619789:4643.97:rs4475691
1   846864  rs950122    G   C   .   PASS    .   ES:SE:LP:SS:ID  -0.022:0.074:0.113509:1697.92:rs950122
1   854250  rs7537756   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.018:0.045:0.161151:1699.96:rs7537756
1   861808  rs13302982  A   G   .   PASS    .   ES:SE:LP:SS:ID  0.048:0.11:0.187087:1700:rs13302982
1   863124  rs4040604   G   T   .   PASS    .   ES:SE:LP:SS:ID  0.012:0.11:0.0409586:1699.99:rs4040604
1   870645  rs28576697  T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.025:0.04:0.267606:1699.57:rs28576697
1   879317  rs7523549   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.024:0.11:0.0861861:1699.91:rs7523549
1   880238  rs3748592   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.026:0.078:0.130768:1699.92:rs3748592
1   880390  rs3748593   C   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0031:0.11:0.00877392:1700:rs3748593
1   882033  rs2272756   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.016:0.042:0.161151:1699.98:rs2272756
1   882803  rs2340582   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.036:0.078:0.187087:1699.98:rs2340582
1   884815  rs4246503   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.035:0.078:0.187087:1699.99:rs4246503
1   886384  rs3748594   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0047:0.11:0.0132283:1699.99:rs3748594
1   887560  rs3748595   A   C   .   PASS    .   ES:SE:LP:SS:ID  -0.013:0.074:0.0655015:1699.93:rs3748595
1   888659  rs3748597   T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.016:0.06:0.102373:2906:rs3748597
1   891945  rs13303106  A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0078:0.037:0.0809219:1699.98:rs13303106
1   893981  rs28415373  C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.21:0.2:0.49485:1699.91:rs28415373
1   894573  rs13303010  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.033:0.06:0.236572:1699.75:rs13303010
1   900505  rs28705211  G   C   .   PASS    .   ES:SE:LP:SS:ID  0.015:0.024:0.275724:4645.43:rs28705211
1   900730  rs3935066   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.047:0.062:0.346787:1699.76:rs3935066
1   903104  rs6696281   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.05:0.092:0.229148:1699.98:rs6696281
1   908414  rs28504611  C   T   .   PASS    .   ES:SE:LP:SS:ID  0.13:0.11:0.638272:1699.88:rs28504611
1   916834  rs6694632   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.026:0.036:0.327902:1699.91:rs6694632
1   918384  rs13303118  G   T   .   PASS    .   ES:SE:LP:SS:ID  -0.011:0.024:0.19382:3948.76:rs13303118
1   918573  rs2341354   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.055:0.034:1:2018:rs2341354
1   924898  rs6665000   C   A   .   PASS    .   ES:SE:LP:SS:ID  0.081:0.097:0.387216:1700:rs6665000