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-42,TotalVariants=14237637,VariantsNotRead=0,HarmonisedVariants=14237637,VariantsNotHarmonised=0,SwitchedAlleles=6216635,NormalisedVariants=0,TotalControls=43456,TotalCases=33640,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/4e410728-95ea-4c9e-8588-0cf8599c35ce/call-vcf/inputs/562856220/upload.txt.gz --id ieu-b-42 --json /data/cromwell-executions/qc/4e410728-95ea-4c9e-8588-0cf8599c35ce/call-vcf/inputs/562856220/ieu-b-42_data.json --ref /data/cromwell-executions/qc/4e410728-95ea-4c9e-8588-0cf8599c35ce/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/4e410728-95ea-4c9e-8588-0cf8599c35ce/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-42/ieu-b-42.vcf.gz --rm_chr_prefix --cohort_cases 33640 --cohort_controls 43456; 1.2.1",
    "file_date": "2020-08-21T23:44:39.540289",
    "bcftools_viewVersion": "1.9+htslib-1.9",
    "bcftools_viewCommand": "view -h /data/igd/ieu-b-42/ieu-b-42.vcf.gz; Date=Thu Feb 25 02:01:49 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/4e410728-95ea-4c9e-8588-0cf8599c35ce/call-ldsc/inputs/562856220/ieu-b-42.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-42/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Sat Aug 22 00:02:22 2020
Reading summary statistics from /data/cromwell-executions/qc/4e410728-95ea-4c9e-8588-0cf8599c35ce/call-ldsc/inputs/562856220/ieu-b-42.vcf.gz ...
Read summary statistics for 14237418 SNPs.
Dropped 109203 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, 1220686 SNPs remain.
After merging with regression SNP LD, 1220686 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.4552 (0.0165)
Lambda GC: 1.5613
Mean Chi^2: 1.7348
Intercept: 1.0456 (0.0095)
Ratio: 0.0621 (0.013)
Analysis finished at Sat Aug 22 00:04:16 2020
Total time elapsed: 1.0m:54.38s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9595,
    "inflation_factor": 1.1941,
    "mean_EFFECT": 0.0626,
    "n": 77096,
    "n_snps": 14237637,
    "n_clumped_hits": 81,
    "n_p_sig": 12625,
    "n_mono": 1693817,
    "n_ns": 0,
    "n_mac": 1655602,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 452238,
    "n_est": 66851.2629,
    "ratio_se_n": 0.9312,
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": 2.3558,
    "sd_y_est2": 2.1937,
    "r2_sum1": 0.2093,
    "r2_sum2": 0.0377,
    "r2_sum3": 0.0435,
    "r2_sum4": 0.0437,
    "ldsc_nsnp_merge_refpanel_ld": 1220686,
    "ldsc_nsnp_merge_regression_ld": 1220686,
    "ldsc_observed_scale_h2_beta": 0.4552,
    "ldsc_observed_scale_h2_se": 0.0165,
    "ldsc_intercept_beta": 1.0456,
    "ldsc_intercept_se": 0.0095,
    "ldsc_lambda_gc": 1.5613,
    "ldsc_mean_chisq": 1.7348,
    "ldsc_ratio": 0.0621
}
 

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 TRUE
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 102 0.9999928 3 59 0 14211946 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 8.660667e+00 5.772339e+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 7.874250e+07 5.627260e+07 828.0000 3.254248e+07 6.927169e+07 1.144739e+08 2.492395e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 6.262600e-02 5.499043e+00 -707.2710 -2.700200e-02 9.000000e-04 3.130500e-02 7.094110e+02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.933884e+01 6.411964e+02 0.0106 1.480000e-02 3.920000e-02 2.015000e-01 1.299000e+05 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.712639e-01 2.995100e-01 0.0000 2.051002e-01 4.610999e-01 7.306998e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.712637e-01 2.995123e-01 0.0000 2.051112e-01 4.610983e-01 7.306670e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 1.585929e-01 2.456719e-01 0.0000 4.000000e-03 2.600000e-02 2.160000e-01 1.000000e+00 ▇▁▁▁▁
numeric AF_reference 452238 0.9682364 NA NA NA NA NA 1.655272e-01 2.391206e-01 0.0000 5.391400e-03 4.492810e-02 2.318290e-01 1.000000e+00 ▇▁▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 7.709600e+04 0.000000e+00 77096.0000 7.709600e+04 7.709600e+04 7.709600e+04 7.709600e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10611 rs189107123 C G 0.078502 0.0818 0.3366999 0.3372152 0.021 NA 77096
1 13302 rs75241669 C T 0.006698 0.0299 0.8220000 0.8227469 0.137 NA 77096
1 13327 rs2691329 G C 0.007204 0.0538 0.8936001 0.8934790 0.040 NA 77096
1 13980 rs2592732 T C -0.042504 0.0725 0.5577005 0.5576994 0.022 NA 77096
1 30923 rs806731 G T 0.000500 0.0223 0.9812000 0.9821117 0.728 0.8724040 77096
1 51476 rs2531249 T C -0.029102 0.1084 0.7883009 0.7883386 0.008 NA 77096
1 51479 rs116400033 T A -0.016201 0.0235 0.4890002 0.4905689 0.215 0.1281950 77096
1 52058 rs1199236530 G C 0.036602 0.0472 0.4378002 0.4380643 0.049 NA 77096
1 52144 rs190291950 T A -0.077702 0.0959 0.4177996 0.4178023 0.015 0.0009984 77096
1 52238 rs2691277 T G -0.005803 0.0418 0.8891000 0.8895863 0.951 0.9217250 77096
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51233300 rs9616839 C T 0.029297 0.0161 0.0679595 0.0688063 0.272 0.3146960 77096
22 51234048 rs141330630 T C 0.711494 0.7451 0.3396002 0.3396296 0.001 0.0095847 77096
22 51234159 rs8138356 T A 0.119799 0.1138 0.2921999 0.2924715 0.001 0.0215655 77096
22 51234677 rs189571549 A C 0.094399 0.1029 0.3587996 0.3589405 0.001 0.0227636 77096
22 51234799 rs191117135 G A -0.019499 0.0936 0.8351000 0.8349770 0.013 0.0059904 77096
22 51237063 rs3896457 T C 0.017095 0.0165 0.3008999 0.3001739 0.255 0.2050720 77096
22 51237069 rs183661957 T C 4.556380 3.2500 0.1609000 0.1609263 0.000 0.0029952 77096
22 51238249 rs149733995 A C 0.034995 0.0290 0.2267003 0.2275384 0.067 NA 77096
22 51242613 rs140611932 A C 4.556380 3.2500 0.1609000 0.1609263 0.000 NA 77096
22 51243297 rs1555938782 A T -0.045403 0.0241 0.0599998 0.0595728 0.148 NA 77096

bcf preview

1   10611   rs189107123 C   G   .   PASS    AF=0.021    ES:SE:LP:AF:SS:NC:ID    0.078502:0.0818:0.472757:0.021:77096:33640:rs189107123
1   13302   rs75241669  C   T   .   PASS    AF=0.137    ES:SE:LP:AF:SS:NC:ID    0.006698:0.0299:0.0851282:0.137:77096:33640:rs75241669
1   13327   rs2691329   G   C   .   PASS    AF=0.04 ES:SE:LP:AF:SS:NC:ID    0.007204:0.0538:0.0488568:0.04:77096:33640:rs2691329
1   13980   rs2592732   T   C   .   PASS    AF=0.022    ES:SE:LP:AF:SS:NC:ID    -0.042504:0.0725:0.253599:0.022:77096:33640:rs2592732
1   30923   rs1165072081    G   T   .   PASS    AF=0.728    ES:SE:LP:AF:SS:NC:ID    0.0005:0.0223:0.00824246:0.728:77096:33640:rs1165072081
1   51476   rs2531249   T   C   .   PASS    AF=0.008    ES:SE:LP:AF:SS:NC:ID    -0.029102:0.1084:0.103308:0.008:77096:33640:rs2531249
1   51479   rs116400033 T   A   .   PASS    AF=0.215    ES:SE:LP:AF:SS:NC:ID    -0.016201:0.0235:0.310691:0.215:77096:33640:rs116400033
1   52058   rs1199236530    G   C   .   PASS    AF=0.049    ES:SE:LP:AF:SS:NC:ID    0.036602:0.0472:0.358724:0.049:77096:33640:rs1199236530
1   52144   rs190291950 T   A   .   PASS    AF=0.015    ES:SE:LP:AF:SS:NC:ID    -0.077702:0.0959:0.379032:0.015:77096:33640:rs190291950
1   52238   rs2691277   T   G   .   PASS    AF=0.951    ES:SE:LP:AF:SS:NC:ID    -0.005803:0.0418:0.0510494:0.951:77096:33640:rs2691277
1   54353   rs140052487 C   A   .   PASS    AF=0.001    ES:SE:LP:AF:SS:NC:ID    1.5385:1.139:0.752518:0.001:77096:33640:rs140052487
1   54421   rs146477069 A   G   .   PASS    AF=0.024    ES:SE:LP:AF:SS:NC:ID    0.024703:0.0429:0.24849:0.024:77096:33640:rs146477069
1   54490   rs141149254 G   A   .   PASS    AF=0.153    ES:SE:LP:AF:SS:NC:ID    -0.009505:0.0261:0.145694:0.153:77096:33640:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.181    ES:SE:LP:AF:SS:NC:ID    0.022202:0.0245:0.436756:0.181:77096:33640:rs2462492
1   54753   rs1472236223    T   G   .   PASS    AF=0.025    ES:SE:LP:AF:SS:NC:ID    0.045604:0.0609:0.342562:0.025:77096:33640:rs1472236223
1   55164   rs3091274   C   A   .   PASS    AF=0.958    ES:SE:LP:AF:SS:NC:ID    -0.006099:0.0452:0.0495378:0.958:77096:33640:rs3091274
1   55299   rs10399749  C   T   .   PASS    AF=0.129    ES:SE:LP:AF:SS:NC:ID    0.009505:0.0246:0.155834:0.129:77096:33640:rs10399749
1   55326   rs3107975   T   C   .   PASS    AF=0.009    ES:SE:LP:AF:SS:NC:ID    -0.036197:0.0587:0.26946:0.009:77096:33640:rs3107975
1   55394   rs2949420   T   A   .   PASS    AF=0.016    ES:SE:LP:AF:SS:NC:ID    -0.063004:0.082:0.354087:0.016:77096:33640:rs2949420
1   55816   rs3020699   G   A   .   PASS    AF=0.011    ES:SE:LP:AF:SS:NC:ID    -0.054604:0.1224:0.183427:0.011:77096:33640:rs3020699
1   55850   rs191890754 C   G   .   PASS    AF=0.007    ES:SE:LP:AF:SS:NC:ID    -0.0305:0.145:0.0790944:0.007:77096:33640:rs191890754
1   55852   rs184233019 G   C   .   PASS    AF=0.001    ES:SE:LP:AF:SS:NC:ID    0.748899:0.615:0.650917:0.001:77096:33640:rs184233019
1   57952   rs2691334   A   C   .   PASS    AF=0.913    ES:SE:LP:AF:SS:NC:ID    -0.070002:0.0336:1.42911:0.913:77096:33640:rs2691334
1   58814   rs114420996 G   A   .   PASS    AF=0.061    ES:SE:LP:AF:SS:NC:ID    -0.040301:0.033:0.652865:0.061:77096:33640:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.057    ES:SE:LP:AF:SS:NC:ID    -0.0256:0.0396:0.286174:0.057:77096:33640:rs62637815
1   60726   rs2531295   C   A   .   PASS    AF=0.034    ES:SE:LP:AF:SS:NC:ID    0.009098:0.0444:0.0766523:0.034:77096:33640:rs2531295
1   61442   rs2531261   A   G   .   PASS    AF=0.988    ES:SE:LP:AF:SS:NC:ID    -0.060003:0.0707:0.402086:0.988:77096:33640:rs2531261
1   61462   rs56992750  T   A   .   PASS    AF=0    ES:SE:LP:AF:SS:NC:ID    -0.067904:0.1326:0.215525:0:77096:33640:rs56992750
1   61743   rs184286948 G   C   .   PASS    AF=0.003    ES:SE:LP:AF:SS:NC:ID    0.071204:1.224:0.0206338:0.003:77096:33640:rs184286948
1   61987   rs76735897  A   G   .   PASS    AF=0.387    ES:SE:LP:AF:SS:NC:ID    0.018704:0.0199:0.458421:0.387:77096:33640:rs76735897
1   61989   rs77573425  G   C   .   PASS    AF=0.387    ES:SE:LP:AF:SS:NC:ID    0.018596:0.0199:0.455064:0.387:77096:33640:rs77573425
1   63671   rs80011619  G   A   .   PASS    AF=0.115    ES:SE:LP:AF:SS:NC:ID    -0.011203:0.0263:0.17412:0.115:77096:33640:rs80011619
1   64649   rs181431124 A   C   .   PASS    AF=0.025    ES:SE:LP:AF:SS:NC:ID    0.007004:0.0702:0.0360234:0.025:77096:33640:rs181431124
1   66162   rs201684885 A   T   .   PASS    AF=0.376    ES:SE:LP:AF:SS:NC:ID    0.0044:0.0202:0.0821795:0.376:77096:33640:rs201684885
1   66176   rs1491257206    T   A   .   PASS    AF=0.001    ES:SE:LP:AF:SS:NC:ID    -0.042302:0.1267:0.131767:0.001:77096:33640:rs1491257206
1   66219   rs1557435148    A   T   .   PASS    AF=0.009    ES:SE:LP:AF:SS:NC:ID    -0.048104:0.0831:0.249723:0.009:77096:33640:rs1557435148
1   66331   rs1557435418    A   C   .   PASS    AF=0    ES:SE:LP:AF:SS:NC:ID    0.201602:0.2541:0.369064:0:77096:33640:rs1557435418
1   66442   rs1227875005    T   A   .   PASS    AF=0.015    ES:SE:LP:AF:SS:NC:ID    0.001399:0.0701:0.00713733:0.015:77096:33640:rs1227875005
1   66457   rs1227875005    T   A   .   PASS    AF=0.011    ES:SE:LP:AF:SS:NC:ID    0.169498:0.0942:1.14249:0.011:77096:33640:rs1227875005
1   66507   rs1268339504    T   A   .   PASS    AF=0.094    ES:SE:LP:AF:SS:NC:ID    -0.050904:0.0323:0.938171:0.094:77096:33640:rs1268339504
1   67181   rs28503582  A   G   .   PASS    AF=0    ES:SE:LP:AF:SS:NC:ID    0.022102:0.1223:0.0673233:0:77096:33640:rs28503582
1   69511   rs2691305   A   G   .   PASS    AF=0.695    ES:SE:LP:AF:SS:NC:ID    0.005495:0.02:0.105352:0.695:77096:33640:rs2691305
1   73841   rs143773730 C   T   .   PASS    AF=0.227    ES:SE:LP:AF:SS:NC:ID    0.045499:0.0224:1.37551:0.227:77096:33640:rs143773730
1   77462   rs2462497   G   A   .   PASS    AF=0.067    ES:SE:LP:AF:SS:NC:ID    0.030801:0.0372:0.389659:0.067:77096:33640:rs2462497
1   77874   rs62641297  G   A   .   PASS    AF=0.042    ES:SE:LP:AF:SS:NC:ID    0.004699:0.0396:0.0430636:0.042:77096:33640:rs62641297
1   77961   rs78385339  G   A   .   PASS    AF=0.026    ES:SE:LP:AF:SS:NC:ID    0.007601:0.0445:0.063436:0.026:77096:33640:rs78385339
1   79033   rs2462495   A   G   .   PASS    AF=0.971    ES:SE:LP:AF:SS:NC:ID    0.022604:0.0466:0.20211:0.971:77096:33640:rs2462495
1   79050   rs2949413   G   T   .   PASS    AF=0.935    ES:SE:LP:AF:SS:NC:ID    0.005296:0.0345:0.0563571:0.935:77096:33640:rs2949413
1   79137   rs143777184 A   T   .   PASS    AF=0    ES:SE:LP:AF:SS:NC:ID    0.312398:0.2165:0.826814:0:77096:33640:rs143777184
1   79772   rs147215883 C   G   .   PASS    AF=0.087    ES:SE:LP:AF:SS:NC:ID    0.021397:0.0354:0.263843:0.087:77096:33640:rs147215883