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-1085,TotalVariants=7481913,VariantsNotRead=0,HarmonisedVariants=7481913,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-1085/ieu-a-1085_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T09:20:47.902213",
    "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-1085/ieu-a-1085.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1085/ieu-a-1085_data.vcf.gz; Date=Tue Feb  4 16:05:39 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-1085/ieu-a-1085.vcf.gz; Date=Sun May 10 06:30:38 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-1085/ieu-a-1085.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-1085/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 09:21:13 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1085/ieu-a-1085.vcf.gz ...
Read summary statistics for 7481913 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, 1234259 SNPs remain.
After merging with regression SNP LD, 1234259 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0379 (0.0159)
Lambda GC: 1.1183
Mean Chi^2: 1.1298
Intercept: 1.1024 (0.0078)
Ratio: 0.7893 (0.0602)
Analysis finished at Wed Feb  5 09:22:29 2020
Total time elapsed: 1.0m:16.48s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.932,
    "inflation_factor": 1.1172,
    "mean_EFFECT": 0,
    "n": 36052,
    "n_snps": 7481913,
    "n_clumped_hits": 7,
    "n_p_sig": 153,
    "n_mono": 0,
    "n_ns": 503785,
    "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": 351700,
    "n_est": 35376.8989,
    "ratio_se_n": 0.9906,
    "mean_diff": 0,
    "ratio_diff": 16.9064,
    "sd_y_est1": 0.4671,
    "sd_y_est2": 0.4627,
    "r2_sum1": 0.0019,
    "r2_sum2": 0.0087,
    "r2_sum3": 0.0088,
    "r2_sum4": 0.0087,
    "ldsc_nsnp_merge_refpanel_ld": 1234259,
    "ldsc_nsnp_merge_regression_ld": 1234259,
    "ldsc_observed_scale_h2_beta": 0.0379,
    "ldsc_observed_scale_h2_se": 0.0159,
    "ldsc_intercept_beta": 1.1024,
    "ldsc_intercept_se": 0.0078,
    "ldsc_lambda_gc": 1.1183,
    "ldsc_mean_chisq": 1.1298,
    "ldsc_ratio": 0.7889
}

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 TRUE
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 59 0 7481912 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 44 0 19630 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 40 0 9815 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.681703e+00 5.775558e+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 7.847136e+07 5.667005e+07 3.02000e+02 3.178035e+07 6.891596e+07 1.144324e+08 2.492391e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.140000e-05 6.601900e-03 -6.62175e-02 -3.620500e-03 -6.500000e-06 3.575100e-03 1.180090e-01 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 5.711200e-03 2.566900e-03 3.33060e-03 3.725100e-03 4.660300e-03 6.965500e-03 2.308620e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.822477e-01 2.936359e-01 0.00000e+00 2.231038e-01 4.758905e-01 7.367820e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.822477e-01 2.936359e-01 0.00000e+00 2.231041e-01 4.758899e-01 7.367817e-01 9.999996e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.913287e-01 2.592639e-01 1.20090e-02 7.335100e-02 2.010460e-01 4.539820e-01 9.870730e-01 ▇▃▂▂▁
numeric AF_reference 351700 0.9529933 NA NA NA NA NA 2.885181e-01 2.504129e-01 0.00000e+00 8.286740e-02 2.112620e-01 4.452880e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 3.605200e+04 0.000000e+00 3.60520e+04 3.605200e+04 3.605200e+04 3.605200e+04 3.605200e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10583 rs58108140 G A 0.0034029 0.0077076 0.6588552 0.6588545 0.158153 NA 36052
1 51479 rs116400033 T A 0.0108971 0.0072451 0.1325669 0.1325657 0.183122 0.1281950 36052
1 54676 rs2462492 C T -0.0159222 0.0079343 0.0447765 0.0447757 0.153919 NA 36052
1 55299 rs10399749 C T -0.0076824 0.0073605 0.2966060 0.2966055 0.177563 NA 36052
1 61987 rs76735897 A G -0.0122878 0.0062170 0.0480994 0.0480996 0.303514 NA 36052
1 61989 rs77573425 G C -0.0122958 0.0062170 0.0479535 0.0479539 0.303512 NA 36052
1 66162 rs62639105 A T -0.0094384 0.0060367 0.1179351 0.1179350 0.329955 NA 36052
1 73841 rs143773730 C T -0.0009135 0.0074509 0.9024231 0.9024227 0.176353 NA 36052
1 82163 rs139113303 G A 0.0143658 0.0106687 0.1781312 0.1781294 0.074582 0.0327476 36052
1 82609 rs149189449 C G 0.0143658 0.0106687 0.1781312 0.1781294 0.074582 0.0327476 36052
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51224600 rs187908482 G A 0.0056764 0.0061457 0.3556706 0.3556710 0.133329 0.0387380 36052
22 51224718 rs189454695 T G 0.0000889 0.0049530 0.9856830 0.9856833 0.231318 NA 36052
22 51227891 rs6010091 G A 0.0007610 0.0039750 0.8481741 0.8481742 0.406363 0.4039540 36052
22 51229805 rs9616985 T C 0.0072660 0.0077363 0.3476250 0.3476255 0.069207 0.0730831 36052
22 51229855 rs144549712 G A -0.0029729 0.0055087 0.5894215 0.5894226 0.148164 0.1160140 36052
22 51236013 rs200507571 A AT 0.0003262 0.0044760 0.9418989 0.9418993 0.263895 0.1487620 36052
22 51237063 rs3896457 T C -0.0028892 0.0043315 0.5047508 0.5047521 0.291447 0.2050720 36052
22 51238249 rs149733995 A C 0.0077582 0.0078375 0.3222337 0.3222343 0.070647 NA 36052
23 57596530 rs36177845 A AT -0.0018928 0.0034645 0.5848305 0.5848311 0.558975 NA 36052
23 100784211 rs188350543 C A 0.0042025 0.0041203 0.3077471 0.3077464 0.748382 0.6498010 36052

bcf preview

1   10583   rs58108140  G   A   .   PASS    AF=0.158153 ES:SE:LP:AF:SS:ID   0.00340286:0.00770758:0.18121:0.158153:36052:rs58108140
1   51479   rs116400033 T   A   .   PASS    AF=0.183122 ES:SE:LP:AF:SS:ID   0.0108971:0.00724512:0.877565:0.183122:36052:rs116400033
1   54676   rs2462492   C   T   .   PASS    AF=0.153919 ES:SE:LP:AF:SS:ID   -0.0159222:0.0079343:1.34895:0.153919:36052:rs2462492
1   55299   rs10399749  C   T   .   PASS    AF=0.177563 ES:SE:LP:AF:SS:ID   -0.00768241:0.00736046:0.52782:0.177563:36052:rs10399749
1   61987   rs76735897  A   G   .   PASS    AF=0.303514 ES:SE:LP:AF:SS:ID   -0.0122878:0.00621699:1.31786:0.303514:36052:rs76735897
1   61989   rs77573425  G   C   .   PASS    AF=0.303512 ES:SE:LP:AF:SS:ID   -0.0122958:0.00621698:1.31918:0.303512:36052:rs77573425
1   66162   rs62639105  A   T   .   PASS    AF=0.329955 ES:SE:LP:AF:SS:ID   -0.00943835:0.00603668:0.928357:0.329955:36052:rs62639105
1   73841   rs143773730 C   T   .   PASS    AF=0.176353 ES:SE:LP:AF:SS:ID   -0.000913492:0.00745091:0.0445898:0.176353:36052:rs143773730
1   82163   rs139113303 G   A   .   PASS    AF=0.074582 ES:SE:LP:AF:SS:ID   0.0143658:0.0106687:0.74926:0.074582:36052:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.074582 ES:SE:LP:AF:SS:ID   0.0143658:0.0106687:0.74926:0.074582:36052:rs149189449
1   86028   rs114608975 T   C   .   PASS    AF=0.094621 ES:SE:LP:AF:SS:ID   0.00823631:0.00958433:0.408773:0.094621:36052:rs114608975
1   86065   rs116504101 G   C   .   PASS    AF=0.094629 ES:SE:LP:AF:SS:ID   0.00812642:0.00958437:0.401754:0.094629:36052:rs116504101
1   86303   rs2949417   G   T   .   PASS    AF=0.08279  ES:SE:LP:AF:SS:ID   -0.0187542:0.0102669:1.16909:0.08279:36052:rs2949417
1   86331   rs115209712 A   G   .   PASS    AF=0.082575 ES:SE:LP:AF:SS:ID   -0.018644:0.0102796:1.15662:0.082575:36052:rs115209712
1   87409   rs139490478 C   T   .   PASS    AF=0.094644 ES:SE:LP:AF:SS:ID   0.00800137:0.00958452:0.393814:0.094644:36052:rs139490478
1   88172   rs940551    G   A   .   PASS    AF=0.065736 ES:SE:LP:AF:SS:ID   0.0052302:0.0114257:0.189011:0.065736:36052:rs940551
1   88177   rs143215837 G   C   .   PASS    AF=0.065633 ES:SE:LP:AF:SS:ID   0.00495241:0.0114327:0.177255:0.065633:36052:rs143215837
1   88316   rs113759966 G   A   .   PASS    AF=0.065947 ES:SE:LP:AF:SS:ID   0.00602148:0.0114101:0.223528:0.065947:36052:rs113759966
1   88338   rs55700207  G   A   .   PASS    AF=0.089174 ES:SE:LP:AF:SS:ID   0.00260613:0.00989929:0.101085:0.089174:36052:rs55700207
1   88710   rs186575039 C   G   .   PASS    AF=0.094391 ES:SE:LP:AF:SS:ID   0.00948938:0.00960366:0.490658:0.094391:36052:rs186575039
1   89946   rs138808727 A   T   .   PASS    AF=0.15244  ES:SE:LP:AF:SS:ID   0.00507945:0.00797513:0.280517:0.15244:36052:rs138808727
1   91190   rs143856811 G   A   .   PASS    AF=0.093758 ES:SE:LP:AF:SS:ID   0.00868046:0.0096412:0.43423:0.093758:36052:rs143856811
1   92858   rs147061536 G   T   .   PASS    AF=0.157743 ES:SE:LP:AF:SS:ID   0.00444316:0.00780078:0.244916:0.157743:36052:rs147061536
1   98929   rs12184306  A   G   .   PASS    AF=0.080661 ES:SE:LP:AF:SS:ID   -0.0253613:0.0103126:1.85627:0.080661:36052:rs12184306
1   98974   rs12184307  A   G   .   PASS    AF=0.079988 ES:SE:LP:AF:SS:ID   -0.0258108:0.0103781:1.89005:0.079988:36052:rs12184307
1   120983  rs182468771 C   T   .   PASS    AF=0.084269 ES:SE:LP:AF:SS:ID   -0.00283142:0.00990956:0.110649:0.084269:36052:rs182468771
1   121009  rs1851943   C   T   .   PASS    AF=0.131238 ES:SE:LP:AF:SS:ID   0.000678637:0.00827994:0.0293384:0.131238:36052:rs1851943
1   137825  rs147252685 G   A   .   PASS    AF=0.17979  ES:SE:LP:AF:SS:ID   0.00937777:0.00724441:0.708855:0.17979:36052:rs147252685
1   162463  rs143399298 T   C   .   PASS    AF=0.08252  ES:SE:LP:AF:SS:ID   -0.0241424:0.0103218:1.71361:0.08252:36052:rs143399298
1   234432  rs8179455   A   G   .   PASS    AF=0.074895 ES:SE:LP:AF:SS:ID   0.0028993:0.0105153:0.106371:0.074895:36052:rs8179455
1   249275  rs200079338 GT  G   .   PASS    AF=0.865096 ES:SE:LP:AF:SS:ID   0.00665704:0.00841985:0.367385:0.865096:36052:rs200079338
1   251627  rs72502741  AC  A   .   PASS    AF=0.140351 ES:SE:LP:AF:SS:ID   -0.0107968:0.0083215:0.711136:0.140351:36052:rs72502741
1   255923  rs199745078 G   GTC .   PASS    AF=0.266223 ES:SE:LP:AF:SS:ID   -0.00711638:0.00641974:0.572451:0.266223:36052:rs199745078
1   540975  rs80246094  G   A   .   PASS    AF=0.086384 ES:SE:LP:AF:SS:ID   -0.000129917:0.00997436:0.0045368:0.086384:36052:rs80246094
1   662613  rs151190501 G   A   .   PASS    AF=0.022293 ES:SE:LP:AF:SS:ID   -0.0115643:0.0174474:0.294603:0.022293:36052:rs151190501
1   662622  rs61769339  G   A   .   PASS    AF=0.10955  ES:SE:LP:AF:SS:ID   0.0229681:0.00737058:2.73705:0.10955:36052:rs61769339
1   691541  rs201999089 AT  A   .   PASS    AF=0.10754  ES:SE:LP:AF:SS:ID   -0.00322526:0.00860772:0.150035:0.10754:36052:rs201999089
1   693625  rs190214723 T   C   .   PASS    AF=0.044048 ES:SE:LP:AF:SS:ID   0.000789312:0.0131881:0.0212376:0.044048:36052:rs190214723
1   704637  rs142559957 G   A   .   PASS    AF=0.052775 ES:SE:LP:AF:SS:ID   -0.00158721:0.0111474:0.0521861:0.052775:36052:rs142559957
1   718505  rs181440659 G   A   .   PASS    AF=0.03238  ES:SE:LP:AF:SS:ID   -0.00429824:0.0136:0.123801:0.03238:36052:rs181440659
1   722670  rs116030099 T   C   .   PASS    AF=0.101886 ES:SE:LP:AF:SS:ID   -0.00599479:0.00818109:0.333759:0.101886:36052:rs116030099
1   729679  rs4951859   C   G   .   PASS    AF=0.832886 ES:SE:LP:AF:SS:ID   -0.00640064:0.00593554:0.55149:0.832886:36052:rs4951859
1   732809  rs12131618  T   C   .   PASS    AF=0.083236 ES:SE:LP:AF:SS:ID   0.0143285:0.00777994:1.18365:0.083236:36052:rs12131618
1   734349  rs141242758 T   C   .   PASS    AF=0.132061 ES:SE:LP:AF:SS:ID   0.0155058:0.00644472:1.79238:0.132061:36052:rs141242758
1   734462  rs12564807  G   A   .   PASS    AF=0.88634  ES:SE:LP:AF:SS:ID   0.0138319:0.00874023:0.944916:0.88634:36052:rs12564807
1   735682  rs138174321 G   C   .   PASS    AF=0.04706  ES:SE:LP:AF:SS:ID   -0.0252399:0.0129359:1.29209:0.04706:36052:rs138174321
1   736289  rs79010578  T   A   .   PASS    AF=0.134639 ES:SE:LP:AF:SS:ID   0.00511974:0.00649569:0.365932:0.134639:36052:rs79010578
1   742990  rs202009397 C   T   .   PASS    AF=0.070901 ES:SE:LP:AF:SS:ID   0.0253763:0.00893355:2.34646:0.070901:36052:rs202009397
1   743021  rs3964475   T   C   .   PASS    AF=0.277884 ES:SE:LP:AF:SS:ID   -0.00464113:0.0056138:0.388928:0.277884:36052:rs3964475
1   743420  rs201920982 G   A   .   PASS    AF=0.049864 ES:SE:LP:AF:SS:ID   0.0206885:0.0103565:1.33955:0.049864:36052:rs201920982