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=ukb-d-41221_8,TotalVariants=9538968,VariantsNotRead=0,HarmonisedVariants=9538968,VariantsNotHarmonised=0,SwitchedAlleles=206,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/ukb-d-import/processed/ukb-d-41221_8/ukb-d-41221_8_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T15:08:32.247702",
    "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/ukb-d-import/processed/ukb-d-41221_8/ukb-d-41221_8.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-41221_8/ukb-d-41221_8_data.vcf.gz; Date=Mon Nov 25 15:53:45 2019",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-41221_8/ukb-d-41221_8.vcf.gz; Date=Sat May  9 23:12:07 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/ukb-d-import/processed/ukb-d-41221_8/ukb-d-41221_8.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/ukb-d-import/processed/ukb-d-41221_8/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Nov 25 16:52:48 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-41221_8/ukb-d-41221_8.vcf.gz ...
Read summary statistics for 9538968 SNPs.
Dropped 7101 SNPs with duplicated rs numbers.
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, 1273599 SNPs remain.
After merging with regression SNP LD, 1273599 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0219 (0.0585)
Lambda GC: 1.0087
Mean Chi^2: 0.9989
Intercept: 0.9954 (0.0063)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Mon Nov 25 16:54:23 2019
Total time elapsed: 1.0m:35.07s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9391,
    "inflation_factor": 1.0071,
    "mean_EFFECT": -5.4734e-06,
    "n": 8019,
    "n_snps": 9538968,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1053364,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 190719,
    "n_est": 7975.0825,
    "ratio_se_n": 0.9973,
    "mean_diff": -8.8589e-06,
    "ratio_diff": 7.6407,
    "sd_y_est1": 0.3543,
    "sd_y_est2": 0.3533,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1273599,
    "ldsc_nsnp_merge_regression_ld": 1273599,
    "ldsc_observed_scale_h2_beta": 0.0219,
    "ldsc_observed_scale_h2_se": 0.0585,
    "ldsc_intercept_beta": 0.9954,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 1.0087,
    "ldsc_mean_chisq": 0.9989,
    "ldsc_ratio": 4.1818
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique TRUE
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 94 0 9532413 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 98 0 46563 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 29461 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.080854e+00 6.174592e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.871809e+07 5.611168e+07 302.0000000 3.241994e+07 6.959497e+07 1.147364e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -5.500000e-06 1.217030e-02 -0.1029060 -6.027400e-03 -6.680000e-05 5.895000e-03 1.256510e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.067160e-02 5.884500e-03 0.0054205 6.107300e-03 8.070400e-03 1.358360e-02 3.331080e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.991723e-01 2.886145e-01 0.0000002 2.491730e-01 4.984832e-01 7.488503e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.991524e-01 2.886265e-01 0.0000001 2.491387e-01 4.984640e-01 7.488409e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.655688e-01 2.627563e-01 0.0107947 4.729650e-02 1.650500e-01 4.220600e-01 9.892050e-01 ▇▂▂▁▁
numeric AF_reference 190719 0.9800063 NA NA NA NA NA 2.649560e-01 2.535655e-01 0.0000000 5.411340e-02 1.799120e-01 4.171330e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 8.019000e+03 0.000000e+00 8019.0000000 8.019000e+03 8.019000e+03 8.019000e+03 8.019000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0120630 0.0096229 0.2100361 0.2099980 0.1130550 0.1894970 8019
1 693731 rs12238997 A G 0.0144173 0.0091316 0.1144140 0.1143748 0.1173080 0.1417730 8019
1 707522 rs371890604 G C 0.0153890 0.0102645 0.1338490 0.1338101 0.0980666 0.1293930 8019
1 717587 rs144155419 G A 0.0185255 0.0240727 0.4415816 0.4415582 0.0165228 0.0045926 8019
1 730087 rs148120343 T C 0.0241352 0.0127171 0.0577511 0.0577153 0.0577687 0.0127796 8019
1 731718 rs142557973 T C 0.0114349 0.0086944 0.1884821 0.1884422 0.1226090 0.1543530 8019
1 732032 rs61770163 A C 0.0146753 0.0092218 0.1115671 0.1115274 0.1223880 0.1555510 8019
1 734349 rs141242758 T C 0.0116257 0.0086875 0.1808631 0.1808260 0.1219720 0.1525560 8019
1 749963 rs529266287 T TAA -0.0101789 0.0085135 0.2318820 0.2318443 0.8683880 0.7641770 8019
1 751343 rs28544273 T A 0.0108678 0.0084533 0.1986109 0.1985739 0.1243360 0.2426120 8019
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0025614 0.0119961 0.8309280 0.8309219 0.0578411 0.0309934 8019
23 154923374 rs111332691 T A -0.0209352 0.0133037 0.1156110 0.1155713 0.0452051 0.0116556 8019
23 154925045 rs509981 C T 0.0095420 0.0063814 0.1348761 0.1348371 0.2476040 0.3634440 8019
23 154925895 rs538470 C T 0.0099687 0.0065507 0.1281070 0.1280671 0.2436160 0.3634440 8019
23 154927581 rs644138 G A 0.0089431 0.0060393 0.1386951 0.1386551 0.3058830 0.4635760 8019
23 154929412 rs557132 C T 0.0097320 0.0063834 0.1274069 0.1273670 0.2473410 0.3568210 8019
23 154929637 rs35185538 CT C 0.0096670 0.0066691 0.1472299 0.1471905 0.2320720 0.3011920 8019
23 154929952 rs4012982 CAA C 0.0087639 0.0067501 0.1942088 0.1941718 0.2410540 0.3165560 8019
23 154930230 rs781880 A G 0.0095139 0.0063901 0.1365661 0.1365265 0.2474250 0.3618540 8019
23 154930487 rs781879 T A -0.0012232 0.0210370 0.9536339 0.9536322 0.0212077 0.1263580 8019

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.113055 ES:SE:LP:AF:SS:ID   0.012063:0.00962291:0.677706:0.113055:8019:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.117308 ES:SE:LP:AF:SS:ID   0.0144173:0.00913163:0.941521:0.117308:8019:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0980666    ES:SE:LP:AF:SS:ID   0.015389:0.0102645:0.873385:0.0980666:8019:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0165228    ES:SE:LP:AF:SS:ID   0.0185255:0.0240727:0.354989:0.0165228:8019:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0577687    ES:SE:LP:AF:SS:ID   0.0241352:0.0127171:1.23844:0.0577687:8019:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122609 ES:SE:LP:AF:SS:ID   0.0114349:0.00869441:0.72473:0.122609:8019:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122388 ES:SE:LP:AF:SS:ID   0.0146753:0.00922183:0.952464:0.122388:8019:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121972 ES:SE:LP:AF:SS:ID   0.0116257:0.00868746:0.74265:0.121972:8019:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868388 ES:SE:LP:AF:SS:ID   -0.0101789:0.00851348:0.634733:0.868388:8019:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.124336 ES:SE:LP:AF:SS:ID   0.0108678:0.00845332:0.701997:0.124336:8019:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143495 ES:SE:LP:AF:SS:ID   0.0077574:0.008407:0.448337:0.143495:8019:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.124553 ES:SE:LP:AF:SS:ID   0.0105768:0.00843876:0.677549:0.124553:8019:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869404 ES:SE:LP:AF:SS:ID   -0.00750936:0.00822576:0.44211:0.869404:8019:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.873832 ES:SE:LP:AF:SS:ID   -0.00989649:0.00836761:0.625329:0.873832:8019:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.130327 ES:SE:LP:AF:SS:ID   0.00750082:0.00824504:0.440108:0.130327:8019:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0384088    ES:SE:LP:AF:SS:ID   -0.0227852:0.0147335:0.913551:0.0384088:8019:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.868986 ES:SE:LP:AF:SS:ID   -0.00729645:0.00821915:0.426306:0.868986:8019:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869114 ES:SE:LP:AF:SS:ID   -0.00746153:0.00822157:0.438732:0.869114:8019:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86898  ES:SE:LP:AF:SS:ID   -0.00727697:0.00821856:0.424869:0.86898:8019:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.868925 ES:SE:LP:AF:SS:ID   -0.00720311:0.00819957:0.420545:0.868925:8019:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.127476 ES:SE:LP:AF:SS:ID   0.00854442:0.0083669:0.512603:0.127476:8019:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.868562 ES:SE:LP:AF:SS:ID   -0.00741156:0.00818189:0.437656:0.868562:8019:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867734 ES:SE:LP:AF:SS:ID   -0.00667755:0.00817758:0.382791:0.867734:8019:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.868636 ES:SE:LP:AF:SS:ID   -0.00698532:0.00818674:0.405003:0.868636:8019:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.868641 ES:SE:LP:AF:SS:ID   -0.00698829:0.00818705:0.405205:0.868641:8019:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.868648 ES:SE:LP:AF:SS:ID   -0.00699209:0.00818742:0.405466:0.868648:8019:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869076 ES:SE:LP:AF:SS:ID   -0.00726654:0.00820737:0.424829:0.869076:8019:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991584    ES:SE:LP:AF:SS:ID   0.0102049:0.00959928:0.54095:0.0991584:8019:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873267 ES:SE:LP:AF:SS:ID   -0.00921847:0.00834495:0.56971:0.873267:8019:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862302 ES:SE:LP:AF:SS:ID   -0.00497684:0.00817632:0.265403:0.862302:8019:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.867945 ES:SE:LP:AF:SS:ID   -0.00804761:0.00824071:0.483051:0.867945:8019:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.864723 ES:SE:LP:AF:SS:ID   -0.00829553:0.00825372:0.501833:0.864723:8019:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.099418 ES:SE:LP:AF:SS:ID   0.00889692:0.00990149:0.433064:0.099418:8019:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870233 ES:SE:LP:AF:SS:ID   -0.00830963:0.00835812:0.494638:0.870233:8019:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870233 ES:SE:LP:AF:SS:ID   -0.00830948:0.00835812:0.494626:0.870233:8019:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870229 ES:SE:LP:AF:SS:ID   -0.00830862:0.00835815:0.494556:0.870229:8019:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870636 ES:SE:LP:AF:SS:ID   -0.00845831:0.00836279:0.506061:0.870636:8019:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.127152 ES:SE:LP:AF:SS:ID   0.00876075:0.00836234:0.530422:0.127152:8019:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106066 ES:SE:LP:AF:SS:ID   0.0103037:0.00909071:0.589955:0.106066:8019:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.853117 ES:SE:LP:AF:SS:ID   -0.00735654:0.00815557:0.435251:0.853117:8019:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.835063 ES:SE:LP:AF:SS:ID   -0.00123967:0.00802138:0.0569093:0.835063:8019:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.76113  ES:SE:LP:AF:SS:ID   -0.00261501:0.00647686:0.163416:0.76113:8019:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.106622 ES:SE:LP:AF:SS:ID   -0.00380654:0.00893924:0.173764:0.106622:8019:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.130564 ES:SE:LP:AF:SS:ID   0.00768796:0.00824242:0.454709:0.130564:8019:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.130269 ES:SE:LP:AF:SS:ID   0.0072355:0.00823254:0.420803:0.130269:8019:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.106037 ES:SE:LP:AF:SS:ID   -0.00351601:0.00900337:0.15729:0.106037:8019:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.105209 ES:SE:LP:AF:SS:ID   -0.00347993:0.00907294:0.154083:0.105209:8019:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.827936 ES:SE:LP:AF:SS:ID   -0.00676951:0.0079851:0.401656:0.827936:8019:rs2519006
1   771823  rs2977605   T   C   .   PASS    AF=0.86871  ES:SE:LP:AF:SS:ID   -0.00728433:0.00819964:0.426701:0.86871:8019:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.130385 ES:SE:LP:AF:SS:ID   0.00701453:0.00822743:0.404593:0.130385:8019:rs59066358