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=ieu-a-55,TotalVariants=2509581,VariantsNotRead=0,HarmonisedVariants=2509581,VariantsNotHarmonised=0,SwitchedAlleles=0,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/ieu-a-import/processed/ieu-a-55/ieu-a-55_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T08:09:17.081744",
    "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/ieu-a-import/processed/ieu-a-55/ieu-a-55.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-55/ieu-a-55_data.vcf.gz; Date=Tue Feb  4 10:05:37 2020",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ieu-a-55/ieu-a-55.vcf.gz; Date=Sun May 10 06:42:53 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/ieu-a-import/processed/ieu-a-55/ieu-a-55.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/ieu-a-import/processed/ieu-a-55/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 18:45:55 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-55/ieu-a-55.vcf.gz ...
Read summary statistics for 2509581 SNPs.
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, 1171084 SNPs remain.
After merging with regression SNP LD, 1171084 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1351 (0.0073)
Lambda GC: 1.0584
Mean Chi^2: 1.1994
Intercept: 0.8277 (0.0073)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb  4 18:46:25 2020
Total time elapsed: 30.04s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9177,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -0.0002,
    "n": 211117,
    "n_snps": 2509581,
    "n_clumped_hits": 75,
    "n_p_sig": 1964,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 24374,
    "n_miss_AF_reference": 22117,
    "n_est": 205828.255,
    "ratio_se_n": 0.9874,
    "mean_diff": 0.0001,
    "ratio_diff": 18.8915,
    "sd_y_est1": 1.4777,
    "sd_y_est2": 1.4591,
    "r2_sum1": 0.0275,
    "r2_sum2": 0.0126,
    "r2_sum3": 0.0129,
    "r2_sum4": 0.0201,
    "ldsc_nsnp_merge_refpanel_ld": 1171084,
    "ldsc_nsnp_merge_regression_ld": 1171084,
    "ldsc_observed_scale_h2_beta": 0.1351,
    "ldsc_observed_scale_h2_se": 0.0073,
    "ldsc_intercept_beta": 0.8277,
    "ldsc_intercept_se": 0.0073,
    "ldsc_lambda_gc": 1.0584,
    "ldsc_mean_chisq": 1.1994,
    "ldsc_ratio": -0.8641
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
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 0 1.0000000 3 42 0 2509581 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 8.597213e+00 5.663015e+00 1.0000 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.881153e+07 5.567874e+07 11523.0000 3.265238e+07 7.021015e+07 1.142786e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.082000e-04 9.687000e-03 -0.2400 -4.500000e-03 -1.000000e-04 4.200000e-03 3.90000e-01 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 7.673200e-03 6.346000e-03 0.0035 4.700000e-03 5.600000e-03 7.900000e-03 1.40000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.905817e-01 2.941967e-01 0.0000 2.300001e-01 4.899999e-01 7.499995e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.908959e-01 2.939639e-01 0.0000 2.350305e-01 4.908932e-01 7.451811e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 24374 0.9902876 NA NA NA NA NA 3.553728e-01 2.763704e-01 0.0083 1.167000e-01 2.917000e-01 5.583000e-01 9.91700e-01 ▇▅▃▂▂
numeric AF_reference 22117 0.9911870 NA NA NA NA NA 3.593296e-01 2.571926e-01 0.0000 1.429710e-01 2.961260e-01 5.443290e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.390369e+05 1.905938e+04 50001.0000 1.348430e+05 1.434040e+05 1.437290e+05 2.11117e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.0320 0.0180 0.0819993 0.0754404 0.06780 0.0371406 65000
1 723819 rs11804171 T A -0.0240 0.0210 0.2500000 0.2530979 0.03704 0.1345850 54218
1 752566 rs3094315 G A 0.0027 0.0080 0.7400005 0.7357400 0.84480 0.7182510 81024
1 754192 rs3131968 A G -0.0051 0.0110 0.6400000 0.6429083 0.87500 0.6785140 61307
1 768448 rs12562034 G A 0.0013 0.0140 0.9199999 0.9260171 0.09167 0.1918930 55501
1 775659 rs2905035 A G -0.0002 0.0087 0.9800000 0.9816594 0.87500 0.7450080 88922
1 777122 rs2980319 A T -0.0015 0.0087 0.8600001 0.8631122 0.87500 0.7472040 88914
1 779322 rs4040617 A G -0.0014 0.0097 0.8900000 0.8852400 0.12500 0.2264380 75468
1 780785 rs2977612 T A 0.0014 0.0096 0.8800001 0.8840530 0.86610 0.6693290 77183
1 785050 rs2905062 G A -0.0064 0.0070 0.3599996 0.3605667 NA 0.6269970 120993
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51217134 rs117417021 A G -0.0045 0.0079 0.5700002 0.5689353 0.441700 0.2671730 90531
22 51222100 rs114553188 G T -0.0068 0.0130 0.5999997 0.6009207 0.066700 0.0880591 113765
22 51223637 rs375798137 G A -0.0067 0.0130 0.6100002 0.6062843 0.066700 0.0788738 113763
22 51229805 rs9616985 T C -0.0300 0.0150 0.0479999 0.0455003 0.091700 0.0730831 90905
23 35921591 rs2204667 C G 0.0007 0.0061 0.9100000 0.9086400 0.166700 NA 143627
23 51666786 rs14115 A G 0.0057 0.0100 0.5700002 0.5686777 0.025000 NA 131901
23 70163799 rs1626496 A C -0.0088 0.0088 0.3200000 0.3173105 0.075000 NA 143565
23 74963352 rs1053838 T G 0.0650 0.0620 0.2999998 0.2944603 0.991379 NA 58456
23 91415872 rs6562597 G A -0.0002 0.0170 0.9900000 0.9906133 0.008300 0.0021192 124345
23 118495837 rs12882977 G A -0.0031 0.0045 0.4899999 0.4908932 0.516700 0.2307280 143511

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0678   ES:SE:LP:AF:SS:ID   -0.032:0.018:1.08619:0.0678:65000:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.03704  ES:SE:LP:AF:SS:ID   -0.024:0.021:0.60206:0.03704:54218:rs11804171
1   752566  rs3094315   G   A   .   PASS    AF=0.8448   ES:SE:LP:AF:SS:ID   0.0027:0.008:0.130768:0.8448:81024:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0051:0.011:0.19382:0.875:61307:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.09167  ES:SE:LP:AF:SS:ID   0.0013:0.014:0.0362122:0.09167:55501:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0002:0.0087:0.00877392:0.875:88922:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0015:0.0087:0.0655015:0.875:88914:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   -0.0014:0.0097:0.05061:0.125:75468:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8661   ES:SE:LP:AF:SS:ID   0.0014:0.0096:0.0555173:0.8661:77183:rs2977612
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0064:0.007:0.443698:120993:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8729   ES:SE:LP:AF:SS:ID   0.0026:0.0096:0.102373:0.8729:77123:rs2980300
1   798959  rs11240777  G   A   .   PASS    AF=0.1667   ES:SE:LP:AF:SS:ID   0.0058:0.0098:0.251812:0.1667:73375:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.425    ES:SE:LP:AF:SS:ID   0.0006:0.0091:0.0222764:0.425:64317:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0022:0.0078:0.107905:0.2667:103788:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.0018:0.008:0.0861861:0.15:96191:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   -0.0074:0.0058:0.69897:0.7373:138012:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   -0.0035:0.0073:0.200659:0.1167:108136:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   -0.0004:0.0053:0.0268721:0.5667:139368:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   -0.0007:0.005:0.05061:0.5763:140009:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.09649  ES:SE:LP:AF:SS:ID   -0.0026:0.0075:0.136677:0.09649:108002:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   -0.0015:0.0049:0.119186:0.5917:140108:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   -0.0005:0.0049:0.0362122:0.6017:140119:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   -0.0014:0.0075:0.0705811:0.1271:107870:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   -0.0024:0.0053:0.187087:0.7167:140736:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  -0.0012:0.0077:0.0555173:105761:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   -0.0036:0.0055:0.29243:0.725:140447:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   -0.0027:0.0054:0.207608:0.5667:130679:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.0077:0.0058:0.721246:0.6:107695:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.0053:0.007:0.346787:0.08333:109314:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.08621  ES:SE:LP:AF:SS:ID   0.0074:0.0077:0.481486:0.08621:99998:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   -0.0018:0.0059:0.119186:0.6583:109539:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0099:0.0083:0.619789:0.05:123485:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.008:0.0075:0.537602:0.075:113544:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.009:0.0078:0.60206:0.06667:119819:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05172  ES:SE:LP:AF:SS:ID   0.01:0.0085:0.638272:0.05172:119394:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0065:0.0077:0.39794:0.06667:119723:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.013:0.0088:0.886057:0.05:121243:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   0.0025:0.0073:0.136677:0.3981:84254:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.0063:0.016:0.154902:0.01667:102552:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.012:0.0088:0.744727:0.05833:123370:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.05455  ES:SE:LP:AF:SS:ID   0.013:0.0088:0.823909:0.05455:123380:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.014:0.0089:0.920819:121178:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   0.0077:0.0059:0.69897:0.4123:108205:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.01:0.018:0.236572:0.01667:90816:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5517   ES:SE:LP:AF:SS:ID   -0.0053:0.0058:0.443698:0.5517:107440:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7542   ES:SE:LP:AF:SS:ID   -0.0059:0.0087:0.30103:0.7542:86267:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.0007:0.0079:0.0315171:0.08333:97572:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   -0.007:0.0062:0.585027:0.675:108283:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6833   ES:SE:LP:AF:SS:ID   -0.0069:0.0066:0.522879:0.6833:101509:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.92373  ES:SE:LP:AF:SS:ID   0.0037:0.01:0.142668:0.92373:126141:rs4970357