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-41219_2,TotalVariants=10215585,VariantsNotRead=0,HarmonisedVariants=10215585,VariantsNotHarmonised=0,SwitchedAlleles=214,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-41219_2/ukb-d-41219_2_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T15:08:58.997433",
    "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-41219_2/ukb-d-41219_2.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-41219_2/ukb-d-41219_2_data.vcf.gz; Date=Mon Nov 25 15:36:59 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-41219_2/ukb-d-41219_2.vcf.gz; Date=Sat May  9 14:49:17 2020"
}

LDSC

*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call: 
./ldsc.py \
--h2 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-41219_2/ukb-d-41219_2.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-41219_2/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 16:50:52 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-41219_2/ukb-d-41219_2.vcf.gz ...
Read summary statistics for 10215585 SNPs.
Dropped 7998 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, 1279214 SNPs remain.
After merging with regression SNP LD, 1279214 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.1879 (0.1445)
Lambda GC: 1.0009
Mean Chi^2: 1.0033
Intercept: 1.0157 (0.0063)
Ratio: 4.7717 (1.9025)
Analysis finished at Mon Nov 25 16:52:34 2019
Total time elapsed: 1.0m:42.12s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9426,
    "inflation_factor": 1.0019,
    "mean_EFFECT": 0.0001,
    "n": 3345,
    "n_snps": 10215585,
    "n_clumped_hits": 1,
    "n_p_sig": 14,
    "n_mono": 0,
    "n_ns": 1095535,
    "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": 201506,
    "n_est": 3333.6429,
    "ratio_se_n": 0.9983,
    "mean_diff": 0.0001,
    "ratio_diff": 114.0908,
    "sd_y_est1": 0.4761,
    "sd_y_est2": 0.4753,
    "r2_sum1": 0.0022,
    "r2_sum2": 0.0096,
    "r2_sum3": 0.0096,
    "r2_sum4": 0.0096,
    "ldsc_nsnp_merge_refpanel_ld": 1279214,
    "ldsc_nsnp_merge_regression_ld": 1279214,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0157,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 1.0009,
    "ldsc_mean_chisq": 1.0033,
    "ldsc_ratio": 4.7576
}

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 10208146 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 48844 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 30417 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.078820e+00 6.178055e+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 7.878458e+07 5.607776e+07 302.0000000 3.251512e+07 6.971654e+07 1.147445e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 5.290000e-05 2.955420e-02 -0.2813160 -1.320300e-02 -4.470000e-05 1.314030e-02 3.125390e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.497220e-02 1.580160e-02 0.0112075 1.287050e-02 1.778070e-02 3.251430e-02 8.958560e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.997147e-01 2.889689e-01 0.0000000 2.491747e-01 4.995857e-01 7.499892e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.996667e-01 2.889977e-01 0.0000000 2.490916e-01 4.995380e-01 7.499700e-01 9.999997e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.496732e-01 2.628712e-01 0.0071843 3.497930e-02 1.423320e-01 3.990360e-01 9.928160e-01 ▇▂▂▁▁
numeric AF_reference 201506 0.9802746 NA NA NA NA NA 2.494089e-01 2.537567e-01 0.0000000 3.793930e-02 1.585460e-01 3.955670e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.345000e+03 0.000000e+00 3345.0000000 3.345000e+03 3.345000e+03 3.345000e+03 3.345000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0179785 0.0201576 0.3725143 0.3724482 0.1124020 0.1894970 3345
1 693731 rs12238997 A G -0.0208829 0.0191245 0.2749369 0.2748573 0.1170260 0.1417730 3345
1 707522 rs371890604 G C -0.0217211 0.0217098 0.3171320 0.3170587 0.0975873 0.1293930 3345
1 717587 rs144155419 G A 0.0057822 0.0498476 0.9076621 0.9076548 0.0168393 0.0045926 3345
1 730087 rs148120343 T C -0.0462191 0.0263532 0.0795518 0.0794592 0.0585521 0.0127796 3345
1 731718 rs142557973 T C -0.0178465 0.0181508 0.3255652 0.3254918 0.1229470 0.1543530 3345
1 732032 rs61770163 A C -0.0135815 0.0193893 0.4836888 0.4836378 0.1228790 0.1555510 3345
1 734349 rs141242758 T C -0.0176687 0.0181368 0.3300327 0.3299619 0.1220140 0.1525560 3345
1 749963 rs529266287 T TAA 0.0231661 0.0176817 0.1902261 0.1901370 0.8685380 0.7641770 3345
1 751343 rs28544273 T A -0.0212041 0.0176093 0.2286220 0.2285346 0.1242360 0.2426120 3345
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0354465 0.0253867 0.1627290 0.1626354 0.0569700 0.0309934 3345
23 154923374 rs111332691 T A 0.0407890 0.0275409 0.1386931 0.1385976 0.0457399 0.0116556 3345
23 154925045 rs509981 C T 0.0148564 0.0130546 0.2551961 0.2551120 0.2521760 0.3634440 3345
23 154925895 rs538470 C T 0.0146797 0.0133678 0.2722231 0.2721439 0.2482110 0.3634440 3345
23 154927581 rs644138 G A 0.0049735 0.0124052 0.6885064 0.6884804 0.3095370 0.4635760 3345
23 154929412 rs557132 C T 0.0143934 0.0130559 0.2703491 0.2702686 0.2520330 0.3568210 3345
23 154929637 rs35185538 CT C 0.0167985 0.0137527 0.2219939 0.2219084 0.2348110 0.3011920 3345
23 154929952 rs4012982 CAA C 0.0129094 0.0137926 0.3493599 0.3492909 0.2454930 0.3165560 3345
23 154930230 rs781880 A G 0.0144503 0.0130633 0.2687330 0.2686506 0.2519210 0.3618540 3345
23 154930487 rs781879 T A -0.0251303 0.0432327 0.5610919 0.5610518 0.0218471 0.1263580 3345

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.112402 ES:SE:LP:AF:SS:ID   -0.0179785:0.0201576:0.428857:0.112402:3345:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.117026 ES:SE:LP:AF:SS:ID   -0.0208829:0.0191245:0.560767:0.117026:3345:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0975873    ES:SE:LP:AF:SS:ID   -0.0217211:0.0217098:0.49876:0.0975873:3345:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0168393    ES:SE:LP:AF:SS:ID   0.00578218:0.0498476:0.0420758:0.0168393:3345:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0585521    ES:SE:LP:AF:SS:ID   -0.0462191:0.0263532:1.09935:0.0585521:3345:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122947 ES:SE:LP:AF:SS:ID   -0.0178465:0.0181508:0.487362:0.122947:3345:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122879 ES:SE:LP:AF:SS:ID   -0.0135815:0.0193893:0.315434:0.122879:3345:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.122014 ES:SE:LP:AF:SS:ID   -0.0176687:0.0181368:0.481443:0.122014:3345:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868538 ES:SE:LP:AF:SS:ID   0.0231661:0.0176817:0.72073:0.868538:3345:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.124236 ES:SE:LP:AF:SS:ID   -0.0212041:0.0176093:0.640882:0.124236:3345:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.141999 ES:SE:LP:AF:SS:ID   -0.0251926:0.0176145:0.816024:0.141999:3345:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.124292 ES:SE:LP:AF:SS:ID   -0.0210416:0.0175936:0.634907:0.124292:3345:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869637 ES:SE:LP:AF:SS:ID   0.0201312:0.0171412:0.619237:0.869637:3345:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.873655 ES:SE:LP:AF:SS:ID   0.0184668:0.0173987:0.539722:0.873655:3345:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129651 ES:SE:LP:AF:SS:ID   -0.0236158:0.0172122:0.769183:0.129651:3345:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0415546    ES:SE:LP:AF:SS:ID   0.0638867:0.0295312:1.5145:0.0415546:3345:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869262 ES:SE:LP:AF:SS:ID   0.0208943:0.0171189:0.652971:0.869262:3345:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869262 ES:SE:LP:AF:SS:ID   0.0208358:0.017118:0.650491:0.869262:3345:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869256 ES:SE:LP:AF:SS:ID   0.0208812:0.0171172:0.652496:0.869256:3345:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.868938 ES:SE:LP:AF:SS:ID   0.0189314:0.0170777:0.572339:0.868938:3345:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126814 ES:SE:LP:AF:SS:ID   -0.0214914:0.0174896:0.6591:0.126814:3345:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.868759 ES:SE:LP:AF:SS:ID   0.0187383:0.0170462:0.565861:0.868759:3345:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867793 ES:SE:LP:AF:SS:ID   0.0188825:0.0170256:0.572702:0.867793:3345:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.868643 ES:SE:LP:AF:SS:ID   0.0192724:0.0170502:0.587677:0.868643:3345:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.868646 ES:SE:LP:AF:SS:ID   0.0192843:0.0170513:0.588123:0.868646:3345:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.868658 ES:SE:LP:AF:SS:ID   0.0192632:0.0170525:0.587188:0.868658:3345:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869132 ES:SE:LP:AF:SS:ID   0.0203752:0.0170945:0.631935:0.869132:3345:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0979091    ES:SE:LP:AF:SS:ID   -0.0271077:0.0202889:0.740855:0.0979091:3345:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873294 ES:SE:LP:AF:SS:ID   0.0193403:0.0173856:0.575063:0.873294:3345:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862376 ES:SE:LP:AF:SS:ID   0.0159492:0.0170517:0.456333:0.862376:3345:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868107 ES:SE:LP:AF:SS:ID   0.0198626:0.017211:0.604572:0.868107:3345:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865048 ES:SE:LP:AF:SS:ID   0.0201161:0.017241:0.613694:0.865048:3345:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.100185 ES:SE:LP:AF:SS:ID   -0.0128238:0.0205445:0.273648:0.100185:3345:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870606 ES:SE:LP:AF:SS:ID   0.0213962:0.0174567:0.656771:0.870606:3345:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870606 ES:SE:LP:AF:SS:ID   0.0213983:0.0174567:0.656861:0.870606:3345:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870601 ES:SE:LP:AF:SS:ID   0.0213896:0.0174567:0.656491:0.870601:3345:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870733 ES:SE:LP:AF:SS:ID   0.0211342:0.0174553:0.645751:0.870733:3345:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126593 ES:SE:LP:AF:SS:ID   -0.0225101:0.0174679:0.704195:0.126593:3345:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10536  ES:SE:LP:AF:SS:ID   -0.0240168:0.0191:0.680498:0.10536:3345:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.853371 ES:SE:LP:AF:SS:ID   0.0221504:0.0169368:0.71891:0.853371:3345:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.833954 ES:SE:LP:AF:SS:ID   0.00377308:0.0167285:0.085357:0.833954:3345:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.760547 ES:SE:LP:AF:SS:ID   0.0162915:0.0134993:0.642868:0.760547:3345:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.107623 ES:SE:LP:AF:SS:ID   -0.00772927:0.0185515:0.169431:0.107623:3345:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00814913   ES:SE:LP:AF:SS:ID   -0.0724242:0.0677874:0.54452:0.00814913:3345:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.130185 ES:SE:LP:AF:SS:ID   -0.0228948:0.0171964:0.737172:0.130185:3345:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.1298   ES:SE:LP:AF:SS:ID   -0.0225824:0.0171834:0.723837:0.1298:3345:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.10685  ES:SE:LP:AF:SS:ID   -0.00673509:0.0187046:0.143384:0.10685:3345:rs7518545
1   770181  rs146076599 A   G   .   PASS    AF=0.00941587   ES:SE:LP:AF:SS:ID   0.0094897:0.0654488:0.0531922:0.00941587:3345:rs146076599
1   770377  rs112563271 A   T   .   PASS    AF=0.00815557   ES:SE:LP:AF:SS:ID   -0.0715728:0.0681344:0.532272:0.00815557:3345:rs112563271
1   770886  rs371458725 G   A   .   PASS    AF=0.105814 ES:SE:LP:AF:SS:ID   -0.00636997:0.0188667:0.133321:0.105814:3345:rs371458725