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-1056,TotalVariants=2494720,VariantsNotRead=0,HarmonisedVariants=2494720,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-1056/ieu-a-1056_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T08:07:27.768287",
    "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-1056/ieu-a-1056.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1056/ieu-a-1056_data.vcf.gz; Date=Tue Feb  4 17:12:42 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-1056/ieu-a-1056.vcf.gz; Date=Sat May  9 23:25:47 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-1056/ieu-a-1056.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-1056/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 18:53:18 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1056/ieu-a-1056.vcf.gz ...
Read summary statistics for 2494720 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, 1161251 SNPs remain.
After merging with regression SNP LD, 1161251 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0842 (0.0089)
Lambda GC: 1.1208
Mean Chi^2: 1.1571
Intercept: 1.0112 (0.007)
Ratio: 0.0716 (0.0448)
Analysis finished at Tue Feb  4 18:53:49 2020
Total time elapsed: 30.44s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9335,
    "inflation_factor": 1.1146,
    "mean_EFFECT": -0.0001,
    "n": 93158,
    "n_snps": 2494720,
    "n_clumped_hits": 15,
    "n_p_sig": 557,
    "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": 22169,
    "n_est": 90243.4982,
    "ratio_se_n": 0.9842,
    "mean_diff": 0.0001,
    "ratio_diff": 16.9343,
    "sd_y_est1": 11.4436,
    "sd_y_est2": 11.2632,
    "r2_sum1": 1.2284,
    "r2_sum2": 0.0094,
    "r2_sum3": 0.0097,
    "r2_sum4": 0.0097,
    "ldsc_nsnp_merge_refpanel_ld": 1161251,
    "ldsc_nsnp_merge_regression_ld": 1161251,
    "ldsc_observed_scale_h2_beta": 0.0842,
    "ldsc_observed_scale_h2_se": 0.0089,
    "ldsc_intercept_beta": 1.0112,
    "ldsc_intercept_se": 0.007,
    "ldsc_lambda_gc": 1.1208,
    "ldsc_mean_chisq": 1.1571,
    "ldsc_ratio": 0.0713
}

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 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 42 0 2494720 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 8.599028e+00 5.664801e+00 1.0000 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.880804e+07 5.568628e+07 11523.0000 3.263152e+07 7.022405e+07 1.143092e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.318000e-04 1.096947e-01 -2.6093 -5.140000e-02 1.000000e-04 5.100000e-02 2.84330e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.607210e-02 6.249510e-02 0.0494 5.450000e-02 6.420000e-02 8.950000e-02 1.26770e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.818489e-01 2.936524e-01 0.0000 2.225999e-01 4.764003e-01 7.362003e-01 1.00000e+00 ▇▇▇▇▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.818487e-01 2.936526e-01 0.0000 2.225964e-01 4.764122e-01 7.361598e-01 1.00000e+00 ▇▇▇▇▆
numeric AF 0 1.0000000 NA NA NA NA NA 3.582656e-01 2.683823e-01 0.0028 1.268000e-01 2.934000e-01 5.524000e-01 9.96500e-01 ▇▅▃▃▂
numeric AF_reference 22169 0.9911136 NA NA NA NA NA 3.589976e-01 2.571241e-01 0.0000 1.427720e-01 2.955270e-01 5.437300e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 8.668595e+04 9.021679e+03 30000.9000 8.571430e+04 8.932080e+04 9.270180e+04 9.31580e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C 0.1632 0.2577 0.5266002 0.5265413 0.0609 0.0371406 38540.0
1 723819 rs11804171 T A 0.1410 0.2581 0.5847995 0.5848598 0.0611 0.1345850 38540.0
1 723891 rs2977670 G C -0.1500 0.2696 0.5779004 0.5779512 0.9379 0.7799520 33258.0
1 750235 rs12138618 G A -0.1359 0.2259 0.5474003 0.5474447 0.0672 NA 41182.6
1 752566 rs3094315 G A 0.0165 0.0845 0.8447000 0.8451845 0.8163 0.7182510 67506.0
1 754192 rs3131968 A G 0.0590 0.1121 0.5984998 0.5986688 0.8588 0.6785140 53055.7
1 768448 rs12562034 G A -0.1886 0.1197 0.1150000 0.1151167 0.1434 0.1918930 49964.0
1 775659 rs2905035 A G 0.0799 0.0965 0.4075004 0.4076822 0.8615 0.7450080 69471.0
1 776546 rs12124819 A G -0.0732 0.1194 0.5396995 0.5398331 0.2286 0.0756789 32712.6
1 777122 rs2980319 A T 0.0713 0.0967 0.4606998 0.4609205 0.8618 0.7472040 69471.0
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51217134 rs117417021 A G -0.0020 0.0895 0.9825000 0.9821717 0.4329 0.2671730 59675.9
22 51222100 rs114553188 G T 0.1128 0.1436 0.4320997 0.4321515 0.0617 0.0880591 78779.6
22 51223637 rs375798137 G A 0.1144 0.1444 0.4280998 0.4282186 0.0617 0.0788738 78779.5
22 51229805 rs9616985 T C 0.1100 0.1762 0.5327004 0.5324368 0.0868 0.0730831 56983.0
23 35921591 rs2204667 C G 0.0828 0.0724 0.2528000 0.2527703 0.1600 NA 81980.2
23 51666786 rs14115 A G -0.0206 0.1074 0.8481001 0.8478939 0.0634 NA 88439.4
23 70163799 rs1626496 A C 0.0375 0.1005 0.7090992 0.7090485 0.0783 NA 93095.5
23 74963352 rs1053838 T G 0.6380 0.6466 0.3238001 0.3237899 0.9924 NA 36474.0
23 91415872 rs6562597 G A 0.0904 0.2097 0.6664998 0.6664015 0.0240 0.0021192 70780.9
23 118495837 rs12882977 G A 0.0574 0.0512 0.2627000 0.2622480 0.4638 0.2307280 91244.2

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0609   ES:SE:LP:AF:SS:ID   0.1632:0.2577:0.278519:0.0609:38540:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.0611   ES:SE:LP:AF:SS:ID   0.141:0.2581:0.232993:0.0611:38540:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.9379   ES:SE:LP:AF:SS:ID   -0.15:0.2696:0.238147:0.9379:33258:rs2977670
1   750235  rs12138618  G   A   .   PASS    AF=0.0672   ES:SE:LP:AF:SS:ID   -0.1359:0.2259:0.261695:0.0672:41182.6:rs12138618
1   752566  rs3094315   G   A   .   PASS    AF=0.8163   ES:SE:LP:AF:SS:ID   0.0165:0.0845:0.0732975:0.8163:67506:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.8588   ES:SE:LP:AF:SS:ID   0.059:0.1121:0.222936:0.8588:53055.7:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.1434   ES:SE:LP:AF:SS:ID   -0.1886:0.1197:0.939302:0.1434:49964:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.8615   ES:SE:LP:AF:SS:ID   0.0799:0.0965:0.389872:0.8615:69471:rs2905035
1   776546  rs12124819  A   G   .   PASS    AF=0.2286   ES:SE:LP:AF:SS:ID   -0.0732:0.1194:0.267848:0.2286:32712.6:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.8618   ES:SE:LP:AF:SS:ID   0.0713:0.0967:0.336582:0.8618:69471:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.1389   ES:SE:LP:AF:SS:ID   -0.0484:0.0992:0.203703:0.1389:66471.9:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8612   ES:SE:LP:AF:SS:ID   0.064:0.1002:0.281831:0.8612:65679.8:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.8583   ES:SE:LP:AF:SS:ID   0.0669:0.1001:0.297569:0.8583:65679.8:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8513   ES:SE:LP:AF:SS:ID   0.0369:0.0969:0.152674:0.8513:66260.8:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.8932   ES:SE:LP:AF:SS:ID   0.1366:0.1583:0.410833:0.8932:45155.1:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1144   ES:SE:LP:AF:SS:ID   -0.1522:0.1597:0.467628:0.1144:44882.5:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.2165   ES:SE:LP:AF:SS:ID   -0.0904:0.1142:0.367847:0.2165:44114:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.4491   ES:SE:LP:AF:SS:ID   -0.1396:0.1009:0.777804:0.4491:52006.9:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.3045   ES:SE:LP:AF:SS:ID   -0.1276:0.0896:0.811353:0.3045:60659.9:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.2137   ES:SE:LP:AF:SS:ID   0.0208:0.0856:0.0926424:0.2137:61246.5:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7437   ES:SE:LP:AF:SS:ID   0.0455:0.0701:0.28693:0.7437:77008:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1969   ES:SE:LP:AF:SS:ID   0.0187:0.0785:0.090765:0.1969:65833.2:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5437   ES:SE:LP:AF:SS:ID   0.0203:0.0628:0.12697:0.5437:83520.4:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.551    ES:SE:LP:AF:SS:ID   0.0429:0.0593:0.328457:0.551:83521:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.1874   ES:SE:LP:AF:SS:ID   0.0073:0.0818:0.0319843:0.1874:69344.8:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5582   ES:SE:LP:AF:SS:ID   0.0366:0.0582:0.275806:0.5582:83521.1:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5586   ES:SE:LP:AF:SS:ID   0.0353:0.0578:0.266722:0.5586:83517.2:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1866   ES:SE:LP:AF:SS:ID   -0.0072:0.0842:0.0306307:0.1866:68844.8:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7283   ES:SE:LP:AF:SS:ID   0.013:0.0626:0.0778457:0.7283:86160.7:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.1862   ES:SE:LP:AF:SS:ID   -0.0419:0.0877:0.198665:0.1862:62390.4:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7364   ES:SE:LP:AF:SS:ID   0.0205:0.0656:0.122226:0.7364:85768.4:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5422   ES:SE:LP:AF:SS:ID   0.0339:0.0662:0.215597:0.5422:72511.5:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.9485   ES:SE:LP:AF:SS:ID   0.7099:0.322:1.56146:0.9485:32315.3:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.6094   ES:SE:LP:AF:SS:ID   0.143:0.0699:1.38998:0.6094:67894.6:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1765   ES:SE:LP:AF:SS:ID   0.1966:0.079:1.89279:0.1765:70765:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.161    ES:SE:LP:AF:SS:ID   0.2064:0.0932:1.57138:0.161:54166.8:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.7309   ES:SE:LP:AF:SS:ID   0.2066:0.0676:2.64936:0.7309:72582.8:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.1105   ES:SE:LP:AF:SS:ID   0.1385:0.0999:0.78094:0.1105:76969.4:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.1435   ES:SE:LP:AF:SS:ID   0.2219:0.0891:1.89483:0.1435:73631.3:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.1364   ES:SE:LP:AF:SS:ID   0.1945:0.0881:1.56607:0.1364:76970.9:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.1035   ES:SE:LP:AF:SS:ID   0.0607:0.0956:0.279593:0.1035:74278.9:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1394   ES:SE:LP:AF:SS:ID   0.1882:0.0853:1.56193:0.1394:76938.9:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.0985   ES:SE:LP:AF:SS:ID   0.1218:0.1062:0.599808:0.0985:69611.5:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3298   ES:SE:LP:AF:SS:ID   -0.2519:0.0865:2.4443:0.3298:47982.4:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.0366   ES:SE:LP:AF:SS:ID   0.2875:0.1934:0.862646:0.0366:56366.6:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.115    ES:SE:LP:AF:SS:ID   0.1261:0.1001:0.682354:0.115:76581.4:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.1089   ES:SE:LP:AF:SS:ID   0.1078:0.1019:0.537752:0.1089:73180:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.1075   ES:SE:LP:AF:SS:ID   0.0895:0.1039:0.410497:0.1075:70517.1:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4046   ES:SE:LP:AF:SS:ID   -0.1047:0.0695:0.880085:0.4046:60161.6:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.0356   ES:SE:LP:AF:SS:ID   0.3047:0.1988:0.902049:0.0356:56370.5:rs9659914