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-4972,TotalVariants=12243455,VariantsNotRead=0,HarmonisedVariants=12243455,VariantsNotHarmonised=0,SwitchedAlleles=102,NormalisedVariants=737,TotalControls=485404,TotalCases=1080,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/0ebc956e-5f50-48db-957f-51e1eb78e208/call-vcf/inputs/-261043394/upload.txt.gz --id ieu-b-4972 --json /data/cromwell-executions/qc/0ebc956e-5f50-48db-957f-51e1eb78e208/call-vcf/inputs/-261043394/ieu-b-4972_data.json --ref /data/cromwell-executions/qc/0ebc956e-5f50-48db-957f-51e1eb78e208/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/0ebc956e-5f50-48db-957f-51e1eb78e208/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-4972/ieu-b-4972.vcf.gz --alias alias.txt --cohort_cases 1080 --cohort_controls 485404; 1.3.0",
    "file_date": "2022-04-23T01:20:26.768255",
    "bcftools_viewVersion": "1.9+htslib-1.9",
    "bcftools_viewCommand": "view -h /data/cromwell-executions/qc/0ebc956e-5f50-48db-957f-51e1eb78e208/call-report/inputs/-261043394/ieu-b-4972.vcf.gz; Date=Sat Apr 23 01:46:23 2022"
}

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/0ebc956e-5f50-48db-957f-51e1eb78e208/call-ldsc/inputs/-261043394/ieu-b-4972.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4972/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Sat Apr 23 01:34:44 2022
Reading summary statistics from /data/cromwell-executions/qc/0ebc956e-5f50-48db-957f-51e1eb78e208/call-ldsc/inputs/-261043394/ieu-b-4972.vcf.gz ...
Read summary statistics for 12242455 SNPs.
Dropped 231337 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
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] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1220578 SNPs remain.
After merging with regression SNP LD, 1220578 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0012 (0.0009)
Lambda GC: 1.0051
Mean Chi^2: 1.0054
Intercept: 0.9935 (0.0063)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Sat Apr 23 01:36:59 2022
Total time elapsed: 2.0m:14.58s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.95,
    "inflation_factor": 1.0105,
    "mean_EFFECT": -0.0023,
    "n": "-Inf",
    "n_snps": 12243455,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1279883,
    "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": 404132,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1220578,
    "ldsc_nsnp_merge_regression_ld": 1220578,
    "ldsc_observed_scale_h2_beta": 0.0012,
    "ldsc_observed_scale_h2_se": 0.0009,
    "ldsc_intercept_beta": 0.9935,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 1.0051,
    "ldsc_mean_chisq": 1.0054,
    "ldsc_ratio": -1.2037
}

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 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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 566 0.9999538 3 58 0 12193976 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 101 0 56052 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 662 0 34525 0 NA NA NA NA NA NA NA NA NA NA
logical N 12243455 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.635976e+00 5.758638e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.869400e+07 5.629935e+07 302.0000000 3.250312e+07 6.911928e+07 1.143454e+08 2.492405e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -2.341300e-03 2.549420e-01 -59.8372000 -6.365520e-02 -1.923800e-03 5.828590e-02 1.347390e+02 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.543351e-01 2.916646e-01 0.0425382 5.163040e-02 8.345900e-02 1.926040e-01 8.083480e+01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.987531e-01 2.884306e-01 0.0000002 2.489087e-01 4.977646e-01 7.485762e-01 9.999999e-01 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.987531e-01 2.884306e-01 0.0000002 2.489085e-01 4.977642e-01 7.485771e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.127960e-01 2.602009e-01 0.0000054 1.457950e-02 8.849730e-02 3.382525e-01 9.999950e-01 ▇▂▁▁▁
numeric AF_reference 404132 0.9669920 NA NA NA NA NA NA NA 2.160787e-01 2.512169e-01 0.0000000 1.357830e-02 1.106230e-01 3.426520e-01 1.000000e+00 ▇▂▁▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10177 rs367896724 A AC 0.0049683 0.0657640 0.9397789 0.9397788 0.3989060 0.4253190 NA
1 10352 rs555500075 T TA 0.0800947 0.0676872 0.2366879 0.2366877 0.3932360 0.4375000 NA
1 11008 rs575272151 C G -0.0875863 0.1122520 0.4352352 0.4352349 0.0862242 0.0880591 NA
1 11012 rs544419019 C G -0.0875863 0.1122520 0.4352352 0.4352349 0.0862242 0.0880591 NA
1 13110 rs540538026 G A 0.0500255 0.1498690 0.7385332 0.7385344 0.0586843 0.0267572 NA
1 13116 rs62635286 T G -0.2479130 0.0884898 0.0050850 0.0050850 0.1891810 0.0970447 NA
1 13118 rs200579949 A G -0.2479130 0.0884898 0.0050850 0.0050850 0.1891810 0.0970447 NA
1 13273 rs531730856 G C -0.1030290 0.1036520 0.3202270 0.3202280 0.1341340 0.0950479 NA
1 14464 rs546169444 A T 0.0647537 0.0944120 0.4927992 0.4927995 0.1568980 0.0958466 NA
1 14599 rs531646671 T A -0.1220090 0.0856133 0.1541243 0.1541233 0.1915570 0.1475640 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51233182 rs4040317 G A 0.0103964 0.0538408 0.8468841 0.8468844 0.3200860 0.2633790 NA
22 51233300 rs9616839 C T -0.0054268 0.0537348 0.9195565 0.9195563 0.3343140 0.3146960 NA
22 51233312 rs62240043 A G -0.0108904 0.0566024 0.8474270 0.8474275 0.2729950 0.2134580 NA
22 51233347 rs62240044 T C -0.0108904 0.0566024 0.8474270 0.8474275 0.2729950 0.2134580 NA
22 51234799 rs191117135 G A -0.1924420 0.1998570 0.3355993 0.3355985 0.0156550 0.0059904 NA
22 51235959 rs200189535 T C -0.0840771 0.0659896 0.2026292 0.2026293 0.1953500 0.1996810 NA
22 51235979 rs62240045 G A 0.1074010 0.0732545 0.1426103 0.1426115 0.2637980 0.2400160 NA
22 51236013 rs200507571 A AT 0.0535868 0.0567618 0.3451374 0.3451367 0.2513400 0.1487620 NA
22 51237063 rs3896457 T C 0.0270249 0.0520321 0.6034885 0.6034895 0.2979820 0.2050720 NA
22 51237712 rs370652263 G A -0.1409050 0.1043990 0.1771206 0.1771194 0.0553522 0.0690895 NA

bcf preview

1   10177   rs1264289758    A   AC  .   PASS    AF=0.398906 ES:SE:LP:AF:ID  0.00496833:0.065764:0.0269743:0.398906:rs1264289758
1   10352   rs1557426776    T   TA  .   PASS    AF=0.393236 ES:SE:LP:AF:ID  0.0800947:0.0676872:0.625824:0.393236:rs1557426776
1   11008   rs575272151 C   G   .   PASS    AF=0.0862242    ES:SE:LP:AF:ID  -0.0875863:0.112252:0.361276:0.0862242:rs575272151
1   11012   rs544419019 C   G   .   PASS    AF=0.0862242    ES:SE:LP:AF:ID  -0.0875863:0.112252:0.361276:0.0862242:rs544419019
1   13110   rs540538026 G   A   .   PASS    AF=0.0586843    ES:SE:LP:AF:ID  0.0500255:0.149869:0.13163:0.0586843:rs540538026
1   13116   rs62635286  T   G   .   PASS    AF=0.189181 ES:SE:LP:AF:ID  -0.247913:0.0884898:2.29371:0.189181:rs62635286
1   13118   rs62028691  A   G   .   PASS    AF=0.189181 ES:SE:LP:AF:ID  -0.247913:0.0884898:2.29371:0.189181:rs62028691
1   13273   rs531730856 G   C   .   PASS    AF=0.134134 ES:SE:LP:AF:ID  -0.103029:0.103652:0.494542:0.134134:rs531730856
1   14464   rs546169444 A   T   .   PASS    AF=0.156898 ES:SE:LP:AF:ID  0.0647537:0.094412:0.30733:0.156898:rs546169444
1   14599   rs707680    T   A   .   PASS    AF=0.191557 ES:SE:LP:AF:ID  -0.122009:0.0856133:0.812129:0.191557:rs707680
1   14604   rs1418508701    A   G   .   PASS    AF=0.191557 ES:SE:LP:AF:ID  -0.122009:0.0856133:0.812129:0.191557:rs1418508701
1   14930   rs6682385   A   G   .   PASS    AF=0.473819 ES:SE:LP:AF:ID  0.0284421:0.0667802:0.173811:0.473819:rs6682385
1   14933   rs199856693 G   A   .   PASS    AF=0.0450802    ES:SE:LP:AF:ID  0.195674:0.16446:0.630552:0.0450802:rs199856693
1   15211   rs3982632   T   G   .   PASS    AF=0.741355 ES:SE:LP:AF:ID  -0.0736255:0.0769632:0.470117:0.741355:rs3982632
1   15820   rs1316988498    G   T   .   PASS    AF=0.275124 ES:SE:LP:AF:ID  0.044:0.0788667:0.238892:0.275124:rs1316988498
1   15903   rs557514207 G   GC  .   PASS    AF=0.41884  ES:SE:LP:AF:ID  0.0409388:0.065331:0.274989:0.41884:rs557514207
1   28590   rs1344649620    T   TTGG    .   PASS    AF=0.956571 ES:SE:LP:AF:ID  0.0658153:0.186236:0.140387:0.956571:rs1344649620
1   30923   rs1165072081    G   T   .   PASS    AF=0.910221 ES:SE:LP:AF:ID  0.10343:0.12296:0.397663:0.910221:rs1165072081
1   47159   rs540662756 T   C   .   PASS    AF=0.0627121    ES:SE:LP:AF:ID  0.0521915:0.139326:0.149992:0.0627121:rs540662756
1   49298   rs10399793  T   C   .   PASS    AF=0.623768 ES:SE:LP:AF:ID  -0.084787:0.0780947:0.556559:0.623768:rs10399793
1   49554   rs539322794 A   G   .   PASS    AF=0.0929554    ES:SE:LP:AF:ID  -0.14251:0.120631:0.624419:0.0929554:rs539322794
1   51479   rs116400033 T   A   .   PASS    AF=0.21326  ES:SE:LP:AF:ID  0.0258437:0.0835769:0.120816:0.21326:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.154391 ES:SE:LP:AF:ID  0.0650638:0.09375:0.311871:0.154391:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.400396 ES:SE:LP:AF:ID  -0.00190659:0.0774709:0.00861187:0.400396:rs2462492
1   54712   rs573184866 T   TTTTC   .   PASS    AF=0.585268 ES:SE:LP:AF:ID  0.0519679:0.061453:0.400393:0.585268:rs573184866
1   54716   rs1166278911    C   T   .   PASS    AF=0.417371 ES:SE:LP:AF:ID  0.0522134:0.0707112:0.336988:0.417371:rs1166278911
1   55545   rs28396308  C   T   .   PASS    AF=0.253777 ES:SE:LP:AF:ID  -0.0693733:0.0795983:0.416282:0.253777:rs28396308
1   58814   rs114420996 G   A   .   PASS    AF=0.0899979    ES:SE:LP:AF:ID  -0.223454:0.121524:1.18078:0.0899979:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.0887883    ES:SE:LP:AF:ID  -0.179769:0.121982:0.852157:0.0887883:rs62637815
1   60351   rs62637817  A   G   .   PASS    AF=0.0809837    ES:SE:LP:AF:ID  -0.272327:0.126351:1.50673:0.0809837:rs62637817
1   62777   rs3844233   A   T   .   PASS    AF=0.438273 ES:SE:LP:AF:ID  0.0329296:0.0672453:0.204571:0.438273:rs3844233
1   63268   rs28664618  T   C   .   PASS    AF=0.382186 ES:SE:LP:AF:ID  -0.0686213:0.0723318:0.464995:0.382186:rs28664618
1   63671   rs80011619  G   A   .   PASS    AF=0.158756 ES:SE:LP:AF:ID  0.0895499:0.0920348:0.480759:0.158756:rs80011619
1   63735   rs61158452  CCTA    C   .   PASS    AF=0.315972 ES:SE:LP:AF:ID  0.0639816:0.0716625:0.42951:0.315972:rs61158452
1   64931   rs62639104  G   A   .   PASS    AF=0.0795793    ES:SE:LP:AF:ID  -0.258718:0.127887:1.36581:0.0795793:rs62639104
1   68082   rs367789441 T   C   .   PASS    AF=0.0707801    ES:SE:LP:AF:ID  0.0610702:0.129632:0.195474:0.0707801:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.0329199    ES:SE:LP:AF:ID  0.185995:0.196475:0.46368:0.0329199:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.0738738    ES:SE:LP:AF:ID  0.0908773:0.127872:0.32123:0.0738738:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.751218 ES:SE:LP:AF:ID  0.0663772:0.0810991:0.383957:0.751218:rs200676709
1   74790   rs13328700  C   G   .   PASS    AF=0.0340921    ES:SE:LP:AF:ID  -0.0854028:0.185319:0.1905:0.0340921:rs13328700
1   74792   rs1335672253    G   A   .   PASS    AF=0.0340921    ES:SE:LP:AF:ID  -0.0854028:0.185319:0.1905:0.0340921:rs1335672253
1   76838   rs563953605 T   G   .   PASS    AF=0.0771356    ES:SE:LP:AF:ID  -0.210284:0.130409:0.971202:0.0771356:rs563953605
1   76854   rs367666799 A   G   .   PASS    AF=0.0775037    ES:SE:LP:AF:ID  -0.0304329:0.12498:0.0927949:0.0775037:rs367666799
1   77866   rs563593912 C   T   .   PASS    AF=0.0769408    ES:SE:LP:AF:ID  -0.213311:0.13046:0.991251:0.0769408:rs563593912
1   77874   rs62641297  G   A   .   PASS    AF=0.0769408    ES:SE:LP:AF:ID  -0.213311:0.13046:0.991251:0.0769408:rs62641297
1   81260   rs571136476 C   T   .   PASS    AF=0.0414632    ES:SE:LP:AF:ID  -0.14143:0.182794:0.357435:0.0414632:rs571136476
1   81587   rs536406113 C   T   .   PASS    AF=0.0609432    ES:SE:LP:AF:ID  0.0631756:0.137997:0.189034:0.0609432:rs536406113
1   82163   rs139113303 G   A   .   PASS    AF=0.0754482    ES:SE:LP:AF:ID  -0.0230746:0.126622:0.0678306:0.0754482:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.0754758    ES:SE:LP:AF:ID  -0.0081318:0.126597:0.0228327:0.0754758:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.352798 ES:SE:LP:AF:ID  0.0127627:0.0725279:0.0653411:0.352798:rs201754587