Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std plot

beta_std_plot

beta_std_plot

Metadata

{
    "fileformat": "VCFv4.2",
    "FILTER": "<ID=PASS,Description=\"All filters passed\">",
    "INFO": "<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">",
    "FORMAT": "<ID=ES,Number=A,Type=Float,Description=\"Effect size estimate relative to the alternative allele\">",
    "FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
    "FORMAT.2": "<ID=LP,Number=A,Type=Float,Description=\"-log10 p-value for effect estimate\">",
    "FORMAT.3": "<ID=AF,Number=A,Type=Float,Description=\"Alternate allele frequency in the association study\">",
    "FORMAT.4": "<ID=SS,Number=A,Type=Float,Description=\"Sample size used to estimate genetic effect\">",
    "FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
    "FORMAT.6": "<ID=SI,Number=A,Type=Float,Description=\"Accuracy score of summary data imputation\">",
    "FORMAT.7": "<ID=NC,Number=A,Type=Float,Description=\"Number of cases used to estimate genetic effect\">",
    "FORMAT.8": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
    "META": "<ID=TotalVariants,Number=1,Type=Integer,Description=\"Total number of variants in input\">",
    "META.1": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
    "META.2": "<ID=HarmonisedVariants,Number=1,Type=Integer,Description=\"Total number of harmonised variants\">",
    "META.3": "<ID=VariantsNotHarmonised,Number=1,Type=Integer,Description=\"Total number of variants that could not be harmonised\">",
    "META.4": "<ID=SwitchedAlleles,Number=1,Type=Integer,Description=\"Total number of variants strand switched\">",
    "META.5": "<ID=TotalControls,Number=1,Type=Integer,Description=\"Total number of controls in the association study\">",
    "META.6": "<ID=TotalCases,Number=1,Type=Integer,Description=\"Total number of cases in the association study\">",
    "META.7": "<ID=StudyType,Number=1,Type=String,Description=\"Type of GWAS study [Continuous or CaseControl]\">",
    "SAMPLE": "<ID=ukb-d-6072_6,TotalVariants=12225670,VariantsNotRead=0,HarmonisedVariants=12225670,VariantsNotHarmonised=0,SwitchedAlleles=226,StudyType=Continuous>",
    "contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
    "contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
    "contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
    "contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
    "contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
    "contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
    "contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
    "contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
    "contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
    "contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
    "contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
    "contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
    "contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
    "contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
    "contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
    "contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
    "contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
    "contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
    "contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
    "contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
    "contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
    "contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
    "contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
    "contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
    "contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
    "contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
    "contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
    "contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
    "contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
    "contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
    "contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
    "contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
    "contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
    "contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
    "contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
    "contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
    "contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
    "contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
    "contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
    "contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
    "contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
    "contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
    "contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
    "contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
    "contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
    "contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
    "contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
    "contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
    "contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
    "contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
    "contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
    "contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
    "contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
    "contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
    "contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
    "contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
    "contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
    "contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
    "contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
    "contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
    "contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
    "contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
    "contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
    "contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
    "contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
    "contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
    "contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
    "contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
    "contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
    "contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
    "contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
    "contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
    "contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
    "contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
    "contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
    "contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
    "contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
    "contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
    "contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
    "contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
    "contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
    "contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
    "contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
    "contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-6072_6/ukb-d-6072_6_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T15:34:57.770165",
    "bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-6072_6/ukb-d-6072_6.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-6072_6/ukb-d-6072_6_data.vcf.gz; Date=Mon Nov 25 16:22:46 2019",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-6072_6/ukb-d-6072_6.vcf.gz; Date=Sun May 10 11:36:43 2020"
}

LDSC

*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call: 
./ldsc.py \
--h2 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-6072_6/ukb-d-6072_6.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-6072_6/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Nov 25 16:57:30 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-6072_6/ukb-d-6072_6.vcf.gz ...
Read summary statistics for 12225670 SNPs.
Dropped 10776 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1283157 SNPs remain.
After merging with regression SNP LD, 1283157 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.002 (0.0082)
Lambda GC: 1.0065
Mean Chi^2: 1.0094
Intercept: 1.0116 (0.0059)
Ratio: 1.2272 (0.623)
Analysis finished at Mon Nov 25 16:59:32 2019
Total time elapsed: 2.0m:1.78s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9496,
    "inflation_factor": 1.0099,
    "mean_EFFECT": -0,
    "n": 54601,
    "n_snps": 12225670,
    "n_clumped_hits": 1,
    "n_p_sig": 4,
    "n_mono": 0,
    "n_ns": 1194520,
    "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": 308413,
    "n_est": 54807.6407,
    "ratio_se_n": 1.0019,
    "mean_diff": -0,
    "ratio_diff": 8.9604,
    "sd_y_est1": 0.3026,
    "sd_y_est2": 0.3032,
    "r2_sum1": 0.0001,
    "r2_sum2": 0.0006,
    "r2_sum3": 0.0006,
    "r2_sum4": 0.0006,
    "ldsc_nsnp_merge_refpanel_ld": 1283157,
    "ldsc_nsnp_merge_regression_ld": 1283157,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0116,
    "ldsc_intercept_se": 0.0059,
    "ldsc_lambda_gc": 1.0065,
    "ldsc_mean_chisq": 1.0094,
    "ldsc_ratio": 1.234
}

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 FALSE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio TRUE
ldsc_intercept_beta FALSE
n_clumped_hits FALSE
r2_sum1 FALSE
r2_sum2 FALSE
r2_sum3 FALSE
r2_sum4 FALSE

Definitions

General metrics

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

se_n metrics

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

r2 metrics

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

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

LDSC metrics

Metrics from LD regression

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

Flags

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

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

Plots

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

Diagnostics

Details

Summary stats

skim_type skim_variable n_missing complete_rate character.min character.max character.empty character.n_unique character.whitespace numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 94 0 12215521 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 53927 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 32323 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.066324e+00 6.184832e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.891835e+07 5.597234e+07 3.02000e+02 3.273523e+07 6.994927e+07 1.147861e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.080000e-05 7.639400e-03 -8.29147e-02 -2.526400e-03 -2.130000e-05 2.448900e-03 1.010750e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 5.796000e-03 4.914400e-03 1.50300e-03 2.117200e-03 3.427000e-03 8.049700e-03 2.884790e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.985950e-01 2.889519e-01 0.00000e+00 2.478318e-01 4.978930e-01 7.491400e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.985921e-01 2.889536e-01 0.00000e+00 2.478269e-01 4.978899e-01 7.491393e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.109185e-01 2.587255e-01 2.25630e-03 1.386020e-02 8.708330e-02 3.343510e-01 9.977440e-01 ▇▂▁▁▁
numeric AF_reference 308413 0.9747733 NA NA NA NA NA 2.127051e-01 2.503346e-01 0.00000e+00 1.058310e-02 1.072280e-01 3.376600e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 5.460100e+04 0.000000e+00 5.46010e+04 5.460100e+04 5.460100e+04 5.460100e+04 5.460100e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0005017 0.0031895 0.8750130 0.8750119 0.1121670 0.1894970 54601
1 693731 rs12238997 A G 0.0004996 0.0030218 0.8686830 0.8686828 0.1172240 0.1417730 54601
1 707522 rs371890604 G C 0.0026966 0.0033903 0.4263861 0.4263813 0.0985402 0.1293930 54601
1 717587 rs144155419 G A 0.0029352 0.0082309 0.7213815 0.7213811 0.0154660 0.0045926 54601
1 730087 rs148120343 T C -0.0024657 0.0042095 0.5580576 0.5580541 0.0572311 0.0127796 54601
1 731718 rs142557973 T C 0.0013495 0.0028681 0.6379873 0.6379846 0.1230760 0.1543530 54601
1 732032 rs61770163 A C 0.0017636 0.0030523 0.5633989 0.5633973 0.1228430 0.1555510 54601
1 734349 rs141242758 T C 0.0012316 0.0028706 0.6678916 0.6678900 0.1222480 0.1525560 54601
1 740284 rs61770167 C T -0.0055979 0.0123136 0.6493906 0.6493873 0.0065623 0.0023962 54601
1 749963 rs529266287 T TAA -0.0013688 0.0028280 0.6283607 0.6283602 0.8682710 0.7641770 54601
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0008857 0.0033707 0.7927441 0.7927428 0.0542740 0.0309934 54601
23 154923374 rs111332691 T A 0.0049251 0.0036639 0.1788780 0.1788723 0.0443124 0.0116556 54601
23 154925045 rs509981 C T -0.0000507 0.0017603 0.9770370 0.9770373 0.2427170 0.3634440 54601
23 154925895 rs538470 C T -0.0002593 0.0017999 0.8854540 0.8854536 0.2391000 0.3634440 54601
23 154927581 rs644138 G A -0.0003234 0.0016558 0.8451481 0.8451471 0.2974210 0.4635760 54601
23 154929412 rs557132 C T -0.0000561 0.0017610 0.9745780 0.9745775 0.2425560 0.3568210 54601
23 154929637 rs35185538 CT C 0.0000829 0.0018386 0.9640561 0.9640557 0.2268210 0.3011920 54601
23 154929952 rs4012982 CAA C -0.0002426 0.0018503 0.8956920 0.8956912 0.2368600 0.3165560 54601
23 154930230 rs781880 A G 0.0001082 0.0017606 0.9509809 0.9509808 0.2429450 0.3618540 54601
23 154930487 rs781879 T A -0.0048380 0.0061660 0.4326762 0.4326724 0.0186678 0.1263580 54601

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.112167 ES:SE:LP:AF:SS:ID   0.000501699:0.00318953:0.0579855:0.112167:54601:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.117224 ES:SE:LP:AF:SS:ID   0.000499603:0.00302182:0.0611387:0.117224:54601:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0985402    ES:SE:LP:AF:SS:ID   0.00269661:0.00339026:0.370197:0.0985402:54601:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015466 ES:SE:LP:AF:SS:ID   0.00293524:0.00823087:0.141835:0.015466:54601:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0572311    ES:SE:LP:AF:SS:ID   -0.00246566:0.00420952:0.253321:0.0572311:54601:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123076 ES:SE:LP:AF:SS:ID   0.00134948:0.00286807:0.195188:0.123076:54601:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122843 ES:SE:LP:AF:SS:ID   0.00176361:0.00305227:0.249184:0.122843:54601:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.122248 ES:SE:LP:AF:SS:ID   0.00123161:0.00287058:0.175294:0.122248:54601:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00656229   ES:SE:LP:AF:SS:ID   -0.00559793:0.0123136:0.187494:0.00656229:54601:rs61770167
1   749963  rs529266287 T   TAA .   PASS    AF=0.868271 ES:SE:LP:AF:SS:ID   -0.00136883:0.00282795:0.201791:0.868271:54601:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.124309 ES:SE:LP:AF:SS:ID   0.00220233:0.00280154:0.364712:0.124309:54601:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143544 ES:SE:LP:AF:SS:ID   0.00115652:0.00278034:0.169129:0.143544:54601:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12444  ES:SE:LP:AF:SS:ID   0.00215709:0.00279703:0.355967:0.12444:54601:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869364 ES:SE:LP:AF:SS:ID   -0.000490266:0.0027247:0.0669153:0.869364:54601:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874135 ES:SE:LP:AF:SS:ID   -0.0019704:0.00276995:0.321598:0.874135:54601:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.130177 ES:SE:LP:AF:SS:ID   0.000752605:0.00273101:0.106309:0.130177:54601:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0366477    ES:SE:LP:AF:SS:ID   -0.00446964:0.00495428:0.435373:0.0366477:54601:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.868994 ES:SE:LP:AF:SS:ID   -0.000305698:0.00272241:0.0406752:0.868994:54601:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869113 ES:SE:LP:AF:SS:ID   -0.000401543:0.0027241:0.0541308:0.869113:54601:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869005 ES:SE:LP:AF:SS:ID   -0.000313965:0.00272231:0.0418262:0.869005:54601:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00525718   ES:SE:LP:AF:SS:ID   -0.00900769:0.0137564:0.290221:0.00525718:54601:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00522769   ES:SE:LP:AF:SS:ID   -0.00905283:0.0137923:0.291079:0.00522769:54601:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00558307   ES:SE:LP:AF:SS:ID   0.00788157:0.0135982:0.250122:0.00558307:54601:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869113 ES:SE:LP:AF:SS:ID   -0.000495611:0.00271794:0.0678765:0.869113:54601:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.127452 ES:SE:LP:AF:SS:ID   0.00127566:0.00277266:0.190133:0.127452:54601:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.868711 ES:SE:LP:AF:SS:ID   -0.000603739:0.00271183:0.0841661:0.868711:54601:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867803 ES:SE:LP:AF:SS:ID   -0.000357288:0.00270759:0.0481682:0.867803:54601:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.868861 ES:SE:LP:AF:SS:ID   -0.000442448:0.00271391:0.0602332:0.868861:54601:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.868867 ES:SE:LP:AF:SS:ID   -0.000440092:0.00271409:0.0598886:0.868867:54601:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.868877 ES:SE:LP:AF:SS:ID   -0.000445693:0.00271419:0.0606964:0.868877:54601:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869274 ES:SE:LP:AF:SS:ID   -0.000490877:0.00272089:0.0671048:0.869274:54601:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.100036 ES:SE:LP:AF:SS:ID   0.00200913:0.00315996:0.27992:0.100036:54601:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0063348    ES:SE:LP:AF:SS:ID   0.0113962:0.0123742:0.447245:0.0063348:54601:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873359 ES:SE:LP:AF:SS:ID   -0.00176043:0.00276227:0.280732:0.873359:54601:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862434 ES:SE:LP:AF:SS:ID   -0.00023448:0.00270782:0.0310527:0.862434:54601:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868143 ES:SE:LP:AF:SS:ID   -0.00083878:0.00273671:0.119626:0.868143:54601:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86478  ES:SE:LP:AF:SS:ID   -0.000545477:0.00273411:0.074757:0.86478:54601:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.099864 ES:SE:LP:AF:SS:ID   0.00171827:0.00327341:0.222107:0.099864:54601:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870135 ES:SE:LP:AF:SS:ID   -0.00176301:0.00276558:0.280823:0.870135:54601:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870135 ES:SE:LP:AF:SS:ID   -0.00176356:0.00276558:0.280932:0.870135:54601:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870132 ES:SE:LP:AF:SS:ID   -0.00176311:0.00276559:0.280841:0.870132:54601:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870557 ES:SE:LP:AF:SS:ID   -0.00177355:0.00276752:0.282641:0.870557:54601:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12686  ES:SE:LP:AF:SS:ID   0.00155774:0.00276999:0.241186:0.12686:54601:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106633 ES:SE:LP:AF:SS:ID   0.0006564:0.00301494:0.0821528:0.106633:54601:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.853891 ES:SE:LP:AF:SS:ID   -0.000825365:0.00271046:0.118764:0.853891:54601:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.8364   ES:SE:LP:AF:SS:ID   -0.00243722:0.00266009:0.444233:0.8364:54601:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.760503 ES:SE:LP:AF:SS:ID   -0.00219763:0.00214112:0.516112:0.760503:54601:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.107232 ES:SE:LP:AF:SS:ID   0.00355328:0.00294043:0.644185:0.107232:54601:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00754421   ES:SE:LP:AF:SS:ID   0.00526628:0.0112023:0.194989:0.00754421:54601:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.130245 ES:SE:LP:AF:SS:ID   0.000622402:0.00273134:0.0863212:0.130245:54601:rs762168062