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-71,TotalVariants=2294034,VariantsNotRead=0,HarmonisedVariants=2294034,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-71/ieu-a-71_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T08:47:58.506137",
    "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-71/ieu-a-71.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-71/ieu-a-71_data.vcf.gz; Date=Tue Feb  4 18:46:05 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-71/ieu-a-71.vcf.gz; Date=Sun May 10 09:24:03 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-71/ieu-a-71.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-71/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 11:28:43 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-71/ieu-a-71.vcf.gz ...
Read summary statistics for 2294034 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, 1091705 SNPs remain.
After merging with regression SNP LD, 1091705 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1661 (0.0108)
Lambda GC: 1.0336
Mean Chi^2: 1.0858
Intercept: 0.8844 (0.0075)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 11:29:12 2020
Total time elapsed: 28.63s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9116,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -0.0001,
    "n": 104079,
    "n_snps": 2294034,
    "n_clumped_hits": 27,
    "n_p_sig": 274,
    "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": 8331,
    "n_miss_AF_reference": 18210,
    "n_est": 102116.3359,
    "ratio_se_n": 0.9905,
    "mean_diff": 0,
    "ratio_diff": 4.4399,
    "sd_y_est1": 1.467,
    "sd_y_est2": 1.4531,
    "r2_sum1": 0.0134,
    "r2_sum2": 0.0062,
    "r2_sum3": 0.0063,
    "r2_sum4": 0.0114,
    "ldsc_nsnp_merge_refpanel_ld": 1091705,
    "ldsc_nsnp_merge_regression_ld": 1091705,
    "ldsc_observed_scale_h2_beta": 0.1661,
    "ldsc_observed_scale_h2_se": 0.0108,
    "ldsc_intercept_beta": 0.8844,
    "ldsc_intercept_se": 0.0075,
    "ldsc_lambda_gc": 1.0336,
    "ldsc_mean_chisq": 1.0858,
    "ldsc_ratio": -1.3473
}

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 2294034 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 8.539775e+00 5.626728e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.894138e+07 5.547247e+07 1.3034e+04 3.295368e+07 7.043194e+07 1.142237e+08 2.491808e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.429000e-04 1.026040e-02 -1.4000e-01 -5.900000e-03 -1.000000e-04 5.700000e-03 1.400000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 9.305900e-03 4.141900e-03 4.7000e-03 6.700000e-03 7.700000e-03 1.000000e-02 4.500000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.936477e-01 2.917258e-01 0.0000e+00 2.399999e-01 4.899999e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.934969e-01 2.915171e-01 0.0000e+00 2.399947e-01 4.923555e-01 7.459807e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 8331 0.9963684 NA NA NA NA NA 3.661063e-01 2.691460e-01 8.3000e-03 1.333000e-01 3.083000e-01 5.667000e-01 9.917000e-01 ▇▅▃▃▂
numeric AF_reference 18210 0.9920620 NA NA NA NA NA 3.683053e-01 2.512988e-01 1.9970e-04 1.567490e-01 3.095050e-01 5.509190e-01 1.000000e+00 ▇▇▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 6.141796e+04 8.227166e+03 5.0000e+04 6.016400e+04 6.107500e+04 6.146100e+04 1.040790e+05 ▅▇▁▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 785050 rs2905062 G A -0.0048 0.0089 0.5900000 0.5896620 NA 0.626997 64267
1 1003629 rs4075116 C T 0.0015 0.0080 0.8499999 0.8512686 0.7373 0.720647 58568
1 1017170 rs3766193 C G 0.0055 0.0075 0.4600002 0.4633551 0.5667 0.575479 59110
1 1017197 rs3766192 C T 0.0071 0.0072 0.3200000 0.3240786 0.5763 0.511182 58855
1 1018562 rs9442371 C T 0.0058 0.0071 0.4100001 0.4139848 0.5917 0.530152 59436
1 1018704 rs9442372 A G 0.0053 0.0072 0.4600002 0.4616631 0.6017 0.611022 58906
1 1021415 rs3737728 A G 0.0076 0.0077 0.3200000 0.3236363 0.7167 0.812700 58766
1 1021695 rs9442398 A G 0.0082 0.0079 0.2999998 0.2992818 0.7250 0.727236 59056
1 1022037 rs6701114 C T 0.0090 0.0079 0.2500000 0.2546029 0.5667 0.586661 53280
1 1036959 rs11579015 T C 0.0024 0.0130 0.8499999 0.8535307 0.0500 0.156949 50183
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51163138 rs715586 C T -0.0039 0.0073 0.5900000 0.5931709 0.1500 0.0902556 94615
22 51165664 rs8137951 G A 0.0047 0.0053 0.3800004 0.3751907 0.2750 0.4063500 101606
22 51175626 rs3810648 A G -0.0073 0.0150 0.6200004 0.6264946 0.0667 0.1084270 51179
22 51178090 rs2285395 G A 0.0130 0.0100 0.2200002 0.1936010 0.0667 0.0666933 96455
22 51196164 rs8136603 A T -0.0047 0.0180 0.8000000 0.7940068 0.0750 0.1427720 50214
23 35921591 rs2204667 C G 0.0130 0.0087 0.1499999 0.1351095 0.1667 NA 61429
23 51666786 rs14115 A G -0.0058 0.0150 0.6899999 0.6990030 0.0250 NA 55140
23 70163799 rs1626496 A C -0.0002 0.0130 0.9900000 0.9877253 0.0750 NA 61441
23 91415872 rs6562597 G A -0.0240 0.0250 0.3300000 0.3370552 0.0083 0.0021192 52407
23 118495837 rs12882977 G A 0.0043 0.0063 0.4899999 0.4948978 0.5167 0.2307280 61362

bcf preview

1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0048:0.0089:0.229148:64267:rs2905062
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.0015:0.008:0.0705811:0.7373:58568:rs4075116
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0055:0.0075:0.337242:0.5667:59110:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.0071:0.0072:0.49485:0.5763:58855:rs3766192
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   0.0058:0.0071:0.387216:0.5917:59436:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   0.0053:0.0072:0.337242:0.6017:58906:rs9442372
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   0.0076:0.0077:0.49485:0.7167:58766:rs3737728
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.0082:0.0079:0.522879:0.725:59056:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.009:0.0079:0.60206:0.5667:53280:rs6701114
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0024:0.013:0.0705811:0.05:50183:rs11579015
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0053:0.013:0.161151:0.05:50706:rs4970409
1   1060608 rs17160824  G   A   .   PASS    AF=0.0583   ES:SE:LP:AF:SS:ID   0.0045:0.013:0.130768:0.0583:50671:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.0546   ES:SE:LP:AF:SS:ID   0.0077:0.013:0.251812:0.0546:50675:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0074:0.013:0.236572:50673:rs12748370
1   1077064 rs4970357   C   A   .   PASS    AF=0.9237   ES:SE:LP:AF:SS:ID   -0.01:0.015:0.29243:0.9237:51038:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.9123   ES:SE:LP:AF:SS:ID   -0.0083:0.013:0.267606:0.9123:53234:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.9661   ES:SE:LP:AF:SS:ID   -0.018:0.017:0.508638:0.9661:54732:rs4970358
1   1097335 rs9442385   T   G   .   PASS    AF=0.9417   ES:SE:LP:AF:SS:ID   -0.012:0.013:0.431798:0.9417:56034:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.9407   ES:SE:LP:AF:SS:ID   -0.0063:0.013:0.207608:0.9407:58303:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.9583   ES:SE:LP:AF:SS:ID   0.011:0.018:0.275724:0.9583:58482:rs1891905
1   1124663 rs6684820   G   A   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   -0.001:0.0083:0.0457575:0.2667:58800:rs6684820
1   1125553 rs10907174  A   T   .   PASS    AF=0.225    ES:SE:LP:AF:SS:ID   0.0032:0.0087:0.148742:0.225:58697:rs10907174
1   1130727 rs10907175  A   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0004:0.012:0.0132283:0.1:59277:rs10907175
1   1135242 rs9729550   A   C   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   0.0011:0.008:0.05061:0.275:58324:rs9729550
1   1138913 rs3819001   T   C   .   PASS    AF=0.0431   ES:SE:LP:AF:SS:ID   -0.017:0.018:0.468521:0.0431:54432:rs3819001
1   1140435 rs1815606   G   T   .   PASS    AF=0.3103   ES:SE:LP:AF:SS:ID   -0.014:0.006:1.72125:0.3103:82299:rs1815606
1   1143657 rs3753348   C   G   .   PASS    AF=0.0333   ES:SE:LP:AF:SS:ID   -0.017:0.02:0.408935:0.0333:55900:rs3753348
1   1152631 rs11721 C   A   .   PASS    AF=0.0833   ES:SE:LP:AF:SS:ID   0.011:0.013:0.420216:0.0833:57598:rs11721
1   1158277 rs3813199   G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0026:0.012:0.0861861:0.1:58770:rs3813199
1   1162435 rs3766186   C   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.004:0.012:0.136677:0.1:59298:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.005:0.01:0.207608:0.15:58725:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.0517   ES:SE:LP:AF:SS:ID   -0.015:0.016:0.468521:0.0517:54065:rs11260562
1   1176597 rs6675798   T   C   .   PASS    AF=0.1083   ES:SE:LP:AF:SS:ID   0.0023:0.013:0.0705811:0.1083:56002:rs6675798
1   1181751 rs6603783   T   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0025:0.012:0.0757207:0.1:58026:rs6603783
1   1192515 rs7524470   A   G   .   PASS    AF=0.0583   ES:SE:LP:AF:SS:ID   -0.014:0.019:0.337242:0.0583:54576:rs7524470
1   1194804 rs11804831  T   C   .   PASS    AF=0.2083   ES:SE:LP:AF:SS:ID   -0.0087:0.0091:0.468521:0.2083:59187:rs11804831
1   1198618 rs12563338  T   A   .   PASS    AF=0.0417   ES:SE:LP:AF:SS:ID   -0.024:0.019:0.721246:0.0417:58256:rs12563338
1   1206343 rs6667923   C   A   .   PASS    AF=0.0583   ES:SE:LP:AF:SS:ID   -0.017:0.018:0.468521:0.0583:59416:rs6667923
1   1206619 rs6668223   C   A   .   PASS    AF=0.0339   ES:SE:LP:AF:SS:ID   -0.012:0.021:0.251812:0.0339:59203:rs6668223
1   1211292 rs6685064   C   T   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.016:0.013:0.69897:0.1:57319:rs6685064
1   1232319 rs604618    G   A   .   PASS    AF=0.0917   ES:SE:LP:AF:SS:ID   -0.019:0.016:0.638272:0.0917:50414:rs604618
1   1474304 rs1571150   C   A   .   PASS    AF=0.3  ES:SE:LP:AF:SS:ID   0.0081:0.007:0.60206:0.3:61254:rs1571150
1   1478153 rs3766180   T   C   .   PASS    AF=0.2417   ES:SE:LP:AF:SS:ID   0.0097:0.0072:0.744727:0.2417:60823:rs3766180
1   1478180 rs3766178   T   C   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0095:0.0072:0.721246:0.2667:60821:rs3766178
1   1481348 rs3766177   T   C   .   PASS    .   ES:SE:LP:SS:ID  0.012:0.0077:0.886057:60578:rs3766177
1   1483010 rs7517401   G   A   .   PASS    AF=0.2833   ES:SE:LP:AF:SS:ID   0.0076:0.0072:0.537602:0.2833:60803:rs7517401
1   1486834 rs3128342   C   A   .   PASS    AF=0.3333   ES:SE:LP:AF:SS:ID   0.0043:0.0074:0.251812:0.3333:55339:rs3128342
1   1489670 rs7531530   C   T   .   PASS    AF=0.25 ES:SE:LP:AF:SS:ID   0.012:0.0075:0.920819:0.25:60322:rs7531530
1   1489928 rs7366884   T   C   .   PASS    AF=0.25 ES:SE:LP:AF:SS:ID   0.011:0.0076:0.79588:0.25:60855:rs7366884
1   1497201 rs3766169   A   C   .   PASS    AF=0.2458   ES:SE:LP:AF:SS:ID   0.0096:0.0072:0.744727:0.2458:61404:rs3766169