Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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-b-41,TotalVariants=12382417,VariantsNotRead=0,HarmonisedVariants=12382417,VariantsNotHarmonised=0,SwitchedAlleles=5445005,NormalisedVariants=0,TotalControls=31358,TotalCases=20352,StudyType=CaseControl>",
    "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>",
    "Gwas2VCF_command": "--data /data/cromwell-executions/qc/17bc5d34-80eb-4d56-ba46-26e48a8cd3cf/call-vcf/inputs/562856219/upload.txt.gz --id ieu-b-41 --json /data/cromwell-executions/qc/17bc5d34-80eb-4d56-ba46-26e48a8cd3cf/call-vcf/inputs/562856219/ieu-b-41_data.json --ref /data/cromwell-executions/qc/17bc5d34-80eb-4d56-ba46-26e48a8cd3cf/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/17bc5d34-80eb-4d56-ba46-26e48a8cd3cf/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-41/ieu-b-41.vcf.gz --rm_chr_prefix --cohort_cases 20352 --cohort_controls 31358; 1.2.1",
    "file_date": "2020-08-21T22:44:52.808233",
    "bcftools_viewVersion": "1.9+htslib-1.9",
    "bcftools_viewCommand": "view -h /data/igd/ieu-b-41/ieu-b-41.vcf.gz; Date=Thu Feb 25 01:35:11 2021"
}

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 /data/cromwell-executions/qc/17bc5d34-80eb-4d56-ba46-26e48a8cd3cf/call-ldsc/inputs/562856219/ieu-b-41.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-41/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Aug 21 23:03:01 2020
Reading summary statistics from /data/cromwell-executions/qc/17bc5d34-80eb-4d56-ba46-26e48a8cd3cf/call-ldsc/inputs/562856219/ieu-b-41.vcf.gz ...
Read summary statistics for 12382194 SNPs.
Dropped 99953 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/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 /data/ref/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1220685 SNPs remain.
After merging with regression SNP LD, 1220685 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.3459 (0.0156)
Lambda GC: 1.3034
Mean Chi^2: 1.3637
Intercept: 1.0194 (0.0077)
Ratio: 0.0534 (0.0212)
Analysis finished at Fri Aug 21 23:04:53 2020
Total time elapsed: 1.0m:52.27s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9559,
    "inflation_factor": 1.134,
    "mean_EFFECT": 0.0088,
    "n": 51710,
    "n_snps": 12382417,
    "n_clumped_hits": 16,
    "n_p_sig": 240,
    "n_mono": 1,
    "n_ns": 0,
    "n_mac": 263227,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 402769,
    "n_est": 50417.7817,
    "ratio_se_n": 0.9874,
    "mean_diff": "-Inf",
    "ratio_diff": "NaN",
    "sd_y_est1": 2.2993,
    "sd_y_est2": 2.2703,
    "r2_sum1": 0.0492,
    "r2_sum2": 0.0093,
    "r2_sum3": 0.0095,
    "r2_sum4": 0.0105,
    "ldsc_nsnp_merge_refpanel_ld": 1220685,
    "ldsc_nsnp_merge_regression_ld": 1220685,
    "ldsc_observed_scale_h2_beta": 0.3459,
    "ldsc_observed_scale_h2_se": 0.0156,
    "ldsc_intercept_beta": 1.0194,
    "ldsc_intercept_se": 0.0077,
    "ldsc_lambda_gc": 1.3034,
    "ldsc_mean_chisq": 1.3637,
    "ldsc_ratio": 0.0533
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio FALSE
ldsc_intercept_beta FALSE
n_clumped_hits FALSE
r2_sum1 FALSE
r2_sum2 FALSE
r2_sum3 FALSE
r2_sum4 FALSE

Definitions

General metrics

  • af_correlation: Correlation coefficient between AF and AF_reference.
  • inflation_factor (lambda): Genomic inflation factor.
  • mean_EFFECT: Mean of EFFECT size.
  • n: Maximum value of reported sample size across all SNPs, \(n\).
  • n_clumped_hits: Number of clumped hits.
  • n_snps: Number of SNPs
  • n_p_sig: Number of SNPs with pvalue below 5e-8.
  • n_mono: Number of monomorphic (MAF == 1 or MAF == 0) SNPs.
  • n_ns: Number of SNPs with nonsense values:
    • alleles other than A, C, G or T.
    • P-values < 0 or > 1.
    • negative or infinite standard errors (<= 0 or = Infinity).
    • infinite beta estimates or allele frequencies < 0 or > 1.
  • n_mac: Number of cases where MAC (\(2 \times N \times MAF\)) is less than 6.
  • is_snpid_unique: true if the combination of ID REF ALT is unique and therefore no duplication in snpid.
  • n_miss_<*>: Number of NA observations for <*> column.

se_n metrics

  • n_est: Estimated sample size value, \(\widehat{n}\).
  • ratio_se_n: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). We expect ratio_se_n to be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.
  • mean_diff: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.
    • \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
    • \({z}_j = \frac{\beta_j}{{se}_j}\),
    • and \(\beta_j\) is the reported effect size.
  • ratio_diff: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff and the mean of diff2 (expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.
    • \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
    • \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
  • sd_y_est1: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.
    • \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
    • \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
    • and \({se}_j\) is the reported standard error.
  • sd_y_est2: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.
    • \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
    • \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),

r2 metrics

Sum of variance explained, calculated from the clumped top hits sample.

  • r2_sum<*>: r2 statistics under various assumptions
    • 1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).
    • 2: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),
    • 3: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),
    • 4: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).

LDSC metrics

Metrics from LD regression

  • ldsc_nsnp_merge_refpanel_ld: Number of remaining SNPs after merging with reference panel LD.
  • ldsc_nsnp_merge_regression_ld: Number of remaining SNPs after merging with regression SNP LD.
  • ldsc_observed_scale_h2_{beta,se} Coefficient value and SE for total observed scale h2.
  • ldsc_intercept_{beta,se}: Coefficient value and SE for intercept. Intercept is expected to be 1.
  • ldsc_lambda_gc: Lambda GC statistics.
  • ldsc_mean_chisq: Mean \(\chi^2\) statistics.
  • ldsc_ratio: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher \(h^2\) per SNP).

Flags

When a metric needs attention, the flag should return TRUE.

  • af_correlation: abs(af_correlation) < 0.7.
  • inflation_factor: inflation_factor > 1.2.
  • n: n (max reported sample size) < 10000.
  • is_snpid_non_unique: NOT is_snpid_unique.
  • mean_EFFECT_nonfinite: mean(EFFECT) is NA, NaN, or Inf.
  • mean_EFFECT_05: abs(mean(EFFECT)) > 0.5.
  • mean_EFFECT_01: abs(mean(EFFECT)) > 0.1.
  • mean_chisq: ldsc_mean_chisq > 1.3 or ldsc_mean_chisq < 0.7.
  • n_p_sig: n_p_sig > 1000.
  • miss_<*>: n_miss_<*> / n_snps > 0.01.
  • ldsc_ratio: ldsc_ratio > 0.5
  • ldsc_intercept_beta: ldsc_intercept_beta > 1.5
  • n_clumped_hits: n_clumped_hits > 1000
  • r2_sum<*>: r2_sum<*> > 0.5

Plots

  • Manhattan plot
    • Red line: \(-log_{10}^{5 \times 10^{-8}}\)
    • Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
  • QQ plot
  • AF plot
  • P-Z plot
  • beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)

Diagnostics

Details

Summary stats

skim_type skim_variable n_missing complete_rate character.min character.max character.empty character.n_unique character.whitespace numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 110 0.9999911 3 59 0 12357171 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 8.666664e+00 5.773755e+00 1.0000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.853619e+07 5.633116e+07 80.0000 3.234684e+07 6.892030e+07 1.142068e+08 2.492395e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 8.819600e-03 5.006294e-01 -45.7722 -2.369900e-02 1.898000e-03 3.069600e-02 1.121650e+02 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 6.110674e-01 2.855158e+01 0.0131 1.710000e-02 3.540000e-02 1.118000e-01 2.557000e+03 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.797090e-01 2.941236e-01 0.0000 2.205002e-01 4.726003e-01 7.339999e-01 1.000000e+00 ▇▇▇▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.797085e-01 2.941254e-01 0.0000 2.205338e-01 4.726531e-01 7.339817e-01 1.000000e+00 ▇▇▇▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 1.801139e-01 2.508572e-01 0.0000 8.161400e-03 4.706390e-02 2.654260e-01 9.996540e-01 ▇▂▁▁▁
numeric AF_reference 402769 0.9674725 NA NA NA NA NA 1.850055e-01 2.454395e-01 0.0000 6.589500e-03 6.749200e-02 2.773560e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 4.094042e+04 1.876209e+04 260.0000 3.868200e+04 5.171000e+04 5.171000e+04 5.171000e+04 ▂▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10611 rs189107123 C G 0.025502 0.1016 0.8019000 0.8018111 0.0160000 NA 51710
1 13302 rs75241669 C T -0.015398 0.0373 0.6802006 0.6797422 0.1170000 NA 51710
1 13327 rs2691329 G C -0.019101 0.0689 0.7813003 0.7816051 0.0335458 NA 51710
1 13980 rs2592732 T C -0.040403 0.0881 0.6462998 0.6465187 0.0186064 NA 51710
1 30923 rs806731 G T 0.005803 0.0281 0.8361000 0.8363906 0.7530000 0.8724040 51710
1 51476 rs2531249 T C -0.319900 0.1446 0.0269799 0.0269453 0.0076064 NA 49357
1 51479 rs116400033 T A -0.007599 0.0294 0.7949999 0.7960447 0.1962130 0.1281950 51710
1 52058 rs1199236530 G C -0.080700 0.0597 0.1765001 0.1764525 0.0417458 NA 51710
1 52144 rs190291950 T A -0.180204 0.1183 0.1278000 0.1276887 0.0116851 0.0009984 51050
1 52238 rs2691277 T G 0.088099 0.0546 0.1065999 0.1066284 0.9449080 0.9217250 51710
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51233300 rs9616839 C T 0.013400 0.0203 0.5084005 0.5091906 0.2933940 0.3146960 51710
22 51234048 rs141330630 T C -0.257398 0.6227 0.6794007 0.6793444 0.0060000 0.0095847 4232
22 51234159 rs8138356 T A 0.106196 0.1173 0.3654004 0.3652870 0.0082698 0.0215655 46524
22 51234677 rs189571549 A C 0.068397 0.1131 0.5453006 0.5453464 0.0083936 0.0227636 47470
22 51234799 rs191117135 G A 0.171303 0.1142 0.1335999 0.1336076 0.0081447 0.0059904 51238
22 51237063 rs3896457 T C 0.028297 0.0212 0.1813001 0.1819536 0.2511810 0.2050720 51710
22 51237069 rs183661957 T C 0.170397 0.5900 0.7727002 0.7727279 0.0050000 0.0029952 3141
22 51238249 rs149733995 A C -0.009396 0.0347 0.7869008 0.7865617 0.0756064 NA 51710
22 51242613 rs140611932 A C 0.173199 0.5901 0.7691995 0.7691340 0.0050000 NA 3141
22 51243297 rs1555938782 A T 0.007004 0.0297 0.8140000 0.8135685 0.1400000 NA 51710

bcf preview

1   10611   rs189107123 C   G   .   PASS    AF=0.016    ES:SE:LP:AF:SS:NC:ID    0.025502:0.1016:0.0958798:0.016:51710:20352:rs189107123
1   13302   rs75241669  C   T   .   PASS    AF=0.117    ES:SE:LP:AF:SS:NC:ID    -0.015398:0.0373:0.167363:0.117:51710:20352:rs75241669
1   13327   rs2691329   G   C   .   PASS    AF=0.0335458    ES:SE:LP:AF:SS:NC:ID    -0.019101:0.0689:0.107182:0.0335458:51710:20352:rs2691329
1   13980   rs2592732   T   C   .   PASS    AF=0.0186064    ES:SE:LP:AF:SS:NC:ID    -0.040403:0.0881:0.189566:0.0186064:51710:20352:rs2592732
1   30923   rs1165072081    G   T   .   PASS    AF=0.753    ES:SE:LP:AF:SS:NC:ID    0.005803:0.0281:0.0777418:0.753:51710:20352:rs1165072081
1   51476   rs2531249   T   C   .   PASS    AF=0.00760642   ES:SE:LP:AF:SS:NC:ID    -0.3199:0.1446:1.56896:0.00760642:49357:19237:rs2531249
1   51479   rs116400033 T   A   .   PASS    AF=0.196213 ES:SE:LP:AF:SS:NC:ID    -0.007599:0.0294:0.0996329:0.196213:51710:20352:rs116400033
1   52058   rs1199236530    G   C   .   PASS    AF=0.0417458    ES:SE:LP:AF:SS:NC:ID    -0.0807:0.0597:0.753255:0.0417458:51710:20352:rs1199236530
1   52144   rs190291950 T   A   .   PASS    AF=0.0116851    ES:SE:LP:AF:SS:NC:ID    -0.180204:0.1183:0.893469:0.0116851:51050:20171:rs190291950
1   52238   rs2691277   T   G   .   PASS    AF=0.944908 ES:SE:LP:AF:SS:NC:ID    0.088099:0.0546:0.972243:0.944908:51710:20352:rs2691277
1   54421   rs146477069 A   G   .   PASS    AF=0.0536064    ES:SE:LP:AF:SS:NC:ID    0.004902:0.0537:0.032452:0.0536064:51710:20352:rs146477069
1   54490   rs141149254 G   A   .   PASS    AF=0.148606 ES:SE:LP:AF:SS:NC:ID    0.006797:0.0326:0.0780016:0.148606:51710:20352:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.176394 ES:SE:LP:AF:SS:NC:ID    -0.029295:0.0307:0.468393:0.176394:51710:20352:rs2462492
1   54753   rs1472236223    T   G   .   PASS    AF=0.027    ES:SE:LP:AF:SS:NC:ID    -0.0618:0.0765:0.377372:0.027:51710:20352:rs1472236223
1   55164   rs3091274   C   A   .   PASS    AF=0.951394 ES:SE:LP:AF:SS:NC:ID    0.058495:0.0585:0.497983:0.951394:51710:20352:rs3091274
1   55299   rs10399749  C   T   .   PASS    AF=0.173787 ES:SE:LP:AF:SS:NC:ID    0.032496:0.0306:0.540306:0.173787:51710:20352:rs10399749
1   55326   rs3107975   T   C   .   PASS    AF=0.021    ES:SE:LP:AF:SS:NC:ID    -0.023599:0.0718:0.129538:0.021:51710:20352:rs3107975
1   55394   rs2949420   T   A   .   PASS    AF=0.0133032    ES:SE:LP:AF:SS:NC:ID    -0.065702:0.0995:0.293368:0.0133032:51710:20352:rs2949420
1   55816   rs3020699   G   A   .   PASS    AF=0.00802301   ES:SE:LP:AF:SS:NC:ID    -0.205205:0.143:0.820448:0.00802301:45373:18371:rs3020699
1   55850   rs191890754 C   G   .   PASS    AF=0.00760642   ES:SE:LP:AF:SS:NC:ID    -0.182097:0.171:0.542118:0.00760642:25915:9678:rs191890754
1   55852   rs184233019 G   C   .   PASS    AF=0.00673598   ES:SE:LP:AF:SS:NC:ID    -0.114401:0.524:0.0823895:0.00673598:4063:1370:rs184233019
1   57952   rs2691334   A   C   .   PASS    AF=0.911857 ES:SE:LP:AF:SS:NC:ID    0.041197:0.0436:0.463063:0.911857:51710:20352:rs2691334
1   58814   rs114420996 G   A   .   PASS    AF=0.0855394    ES:SE:LP:AF:SS:NC:ID    0.014002:0.0418:0.131767:0.0855394:51710:20352:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.064    ES:SE:LP:AF:SS:NC:ID    -0.007502:0.0512:0.0540393:0.064:51710:20352:rs62637815
1   60726   rs2531295   C   A   .   PASS    AF=0.0497883    ES:SE:LP:AF:SS:NC:ID    -0.041103:0.0559:0.334982:0.0497883:51710:20352:rs2531295
1   61442   rs2531261   A   G   .   PASS    AF=0.981197 ES:SE:LP:AF:SS:NC:ID    0.032399:0.1005:0.126738:0.981197:51710:20352:rs2531261
1   61462   rs56992750  T   A   .   PASS    AF=0.00735382   ES:SE:LP:AF:SS:NC:ID    0.159803:0.1926:0.390619:0.00735382:36442:14248:rs56992750
1   61987   rs76735897  A   G   .   PASS    AF=0.347213 ES:SE:LP:AF:SS:NC:ID    -0.045604:0.025:1.16845:0.347213:51710:20352:rs76735897
1   61989   rs77573425  G   C   .   PASS    AF=0.347213 ES:SE:LP:AF:SS:NC:ID    -0.042803:0.0249:1.06485:0.347213:51710:20352:rs77573425
1   63671   rs80011619  G   A   .   PASS    AF=0.146787 ES:SE:LP:AF:SS:NC:ID    0.023297:0.0332:0.316233:0.146787:51710:20352:rs80011619
1   64649   rs181431124 A   C   .   PASS    AF=0.0186064    ES:SE:LP:AF:SS:NC:ID    -0.001099:0.0888:0.00423322:0.0186064:51710:20352:rs181431124
1   66162   rs201684885 A   T   .   PASS    AF=0.333    ES:SE:LP:AF:SS:NC:ID    -0.017899:0.0253:0.319211:0.333:51710:20352:rs201684885
1   66176   rs1491257206    T   A   .   PASS    AF=0.00757297   ES:SE:LP:AF:SS:NC:ID    0.102196:0.1786:0.246187:0.00757297:44414:18177:rs1491257206
1   66219   rs1557435148    A   T   .   PASS    AF=0.016    ES:SE:LP:AF:SS:NC:ID    -0.058703:0.0994:0.255629:0.016:51710:20352:rs1557435148
1   66331   rs1557435418    A   C   .   PASS    AF=0.006    ES:SE:LP:AF:SS:NC:ID    0.205205:0.2868:0.323947:0.006:21630:8219:rs1557435418
1   66442   rs1227875005    T   A   .   PASS    AF=0.0196639    ES:SE:LP:AF:SS:NC:ID    0.021898:0.0916:0.090765:0.0196639:51710:20352:rs1227875005
1   66457   rs1227875005    T   A   .   PASS    AF=0.00905161   ES:SE:LP:AF:SS:NC:ID    -0.054805:0.1368:0.162096:0.00905161:51710:20352:rs1227875005
1   66507   rs1268339504    T   A   .   PASS    AF=0.0981245    ES:SE:LP:AF:SS:NC:ID    0.006399:0.0396:0.0598821:0.0981245:51710:20352:rs1268339504
1   67181   rs28503582  A   G   .   PASS    AF=0.009    ES:SE:LP:AF:SS:NC:ID    0.196696:0.1549:0.690157:0.009:38067:14843:rs28503582
1   69511   rs2691305   A   G   .   PASS    AF=0.675394 ES:SE:LP:AF:SS:NC:ID    0.033598:0.0249:0.748849:0.675394:51710:20352:rs2691305
1   73841   rs143773730 C   T   .   PASS    AF=0.234819 ES:SE:LP:AF:SS:NC:ID    -0.059803:0.0279:1.49336:0.234819:51710:20352:rs143773730
1   77462   rs2462497   G   A   .   PASS    AF=0.0744606    ES:SE:LP:AF:SS:NC:ID    0.025502:0.0476:0.227019:0.0744606:51710:20352:rs2462497
1   77874   rs62641297  G   A   .   PASS    AF=0.0554703    ES:SE:LP:AF:SS:NC:ID    -0.064805:0.051:0.691863:0.0554703:51710:20352:rs62641297
1   77961   rs78385339  G   A   .   PASS    AF=0.0542394    ES:SE:LP:AF:SS:NC:ID    0.064701:0.0555:0.611721:0.0542394:51710:20352:rs78385339
1   79033   rs2462495   A   G   .   PASS    AF=0.957708 ES:SE:LP:AF:SS:NC:ID    0.064304:0.0609:0.535212:0.957708:51710:20352:rs2462495
1   79050   rs2949413   G   T   .   PASS    AF=0.923181 ES:SE:LP:AF:SS:NC:ID    0.080104:0.0449:1.1272:0.923181:51710:20352:rs2949413
1   79137   rs143777184 A   T   .   PASS    AF=0.007    ES:SE:LP:AF:SS:NC:ID    0.363901:0.334:0.559248:0.007:14237:5197:rs143777184
1   79772   rs147215883 C   G   .   PASS    AF=0.0842128    ES:SE:LP:AF:SS:NC:ID    -0.062205:0.0444:0.791827:0.0842128:51710:20352:rs147215883
1   82163   rs139113303 G   A   .   PASS    AF=0.0593595    ES:SE:LP:AF:SS:NC:ID    0.117801:0.049:1.78941:0.0593595:51710:20352:rs139113303
1   82249   rs1851945   A   G   .   PASS    AF=0.0376064    ES:SE:LP:AF:SS:NC:ID    -0.046397:0.0651:0.322211:0.0376064:51710:20352:rs1851945