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-5117,TotalVariants=12321875,VariantsNotRead=0,HarmonisedVariants=12321875,VariantsNotHarmonised=0,SwitchedAlleles=11141410,NormalisedVariants=744,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>",
    "Gwas2VCF_command": "--data /data/cromwell-executions/qc/cc430a5d-4c90-4285-b0ad-3cb3d4ce99d3/call-vcf/inputs/-261021472/upload.txt.gz --id ieu-b-5117 --json /data/cromwell-executions/qc/cc430a5d-4c90-4285-b0ad-3cb3d4ce99d3/call-vcf/inputs/-261021472/ieu-b-5117_data.json --ref /data/cromwell-executions/qc/cc430a5d-4c90-4285-b0ad-3cb3d4ce99d3/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/cc430a5d-4c90-4285-b0ad-3cb3d4ce99d3/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-5117/ieu-b-5117.vcf.gz --alias alias.txt; 1.3.0",
    "file_date": "2024-02-26T18:34:00.290007",
    "bcftools_viewVersion": "1.9+htslib-1.9",
    "bcftools_viewCommand": "view -h /data/cromwell-executions/qc/cc430a5d-4c90-4285-b0ad-3cb3d4ce99d3/call-report/inputs/-261021472/ieu-b-5117.vcf.gz; Date=Mon Feb 26 19:04:32 2024"
}

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/cc430a5d-4c90-4285-b0ad-3cb3d4ce99d3/call-ldsc/inputs/-261021472/ieu-b-5117.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5117/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Mon Feb 26 18:53:25 2024
Reading summary statistics from /data/cromwell-executions/qc/cc430a5d-4c90-4285-b0ad-3cb3d4ce99d3/call-ldsc/inputs/-261021472/ieu-b-5117.vcf.gz ...
Read summary statistics for 0 SNPs.
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.
Traceback (most recent call last):
  File "./ldsc/ldsc.py", line 647, in <module>
    sumstats.estimate_h2(args, log)
  File "/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
    args, log, args.h2)
  File "/ldsc/ldscore/sumstats.py", line 252, in _read_ld_sumstats
    sumstats = _merge_and_log(ref_ld, sumstats, 'reference panel LD', log)
  File "/ldsc/ldscore/sumstats.py", line 238, in _merge_and_log
    raise ValueError(msg.format(N=len(sumstats), F=noun))
ValueError: After merging with reference panel LD, 0 SNPs remain.

Analysis finished at Mon Feb 26 18:54:54 2024
Total time elapsed: 1.0m:28.57s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9503,
    "inflation_factor": 1.4921,
    "mean_EFFECT": 0.0001,
    "n": "-Inf",
    "n_snps": 12321875,
    "n_clumped_hits": 177,
    "n_p_sig": 15705,
    "n_mono": 0,
    "n_ns": 1293897,
    "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": 1423040,
    "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": 0,
    "ldsc_nsnp_merge_regression_ld": "NA",
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": "NA",
    "ldsc_intercept_se": "NA",
    "ldsc_lambda_gc": "NA",
    "ldsc_mean_chisq": "NA",
    "ldsc_ratio": "NA"
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n TRUE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq NA
n_p_sig TRUE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio NA
ldsc_intercept_beta NA
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 675 0.9999452 3 58 0 12276232 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 88 0 17566 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 662 0 71704 0 NA NA NA NA NA NA NA NA NA NA
logical N 12321875 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 8.757492e+00 5.885387e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.871202e+07 5.622121e+07 302.0000000 3.252510e+07 6.928045e+07 1.144492e+08 2.492405e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 5.450000e-05 9.742800e-03 -0.2215480 -3.432100e-03 1.250000e-05 3.476700e-03 1.451740e-01 ▁▁▅▇▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 6.535700e-03 6.270800e-03 0.0018963 2.290100e-03 3.674800e-03 8.477100e-03 9.948140e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.329340e-01 3.056590e-01 0.0000000 1.499999e-01 4.100001e-01 6.999999e-01 1.000000e+00 ▇▅▅▅▅
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.329362e-01 3.056374e-01 0.0000000 1.512040e-01 4.072989e-01 6.972734e-01 9.999998e-01 ▇▅▅▅▅
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.593996e-01 3.020436e-01 0.0008930 1.660000e-02 1.145670e-01 4.379360e-01 9.990810e-01 ▇▂▁▁▁
numeric AF_reference 1423040 0.8845111 NA NA NA NA NA NA NA 2.132160e-01 2.513550e-01 0.0000000 1.218050e-02 1.056310e-01 3.376600e-01 1.000000e+00 ▇▂▁▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10177 rs1264289758 AC A 0.0032369 0.0029279 0.2700001 0.2689237 0.601646 NA NA
1 10352 rs1557426776 TA T 0.0011754 0.0030112 0.6999999 0.6962728 0.606428 NA NA
1 11008 rs575272151 C G 0.0105670 0.0050278 0.0359998 0.0355772 0.085879 0.0880591 NA
1 11012 rs544419019 C G 0.0105670 0.0050278 0.0359998 0.0355772 0.085879 0.0880591 NA
1 13110 rs540538026 G A -0.0057413 0.0066676 0.3900004 0.3891975 0.058602 0.0267572 NA
1 13116 rs62635286 T G -0.0019916 0.0039429 0.6100002 0.6134857 0.189071 0.0970447 NA
1 13118 rs200579949 A G -0.0019916 0.0039429 0.6100002 0.6134857 0.189071 0.0970447 NA
1 13273 rs531730856 G C 0.0083439 0.0046075 0.0700003 0.0701497 0.134175 0.0950479 NA
1 14464 rs546169444 A T -0.0024090 0.0042001 0.5700002 0.5662694 0.156899 0.0958466 NA
1 14599 rs531646671 T A -0.0075087 0.0038299 0.0500000 0.0499325 0.191034 0.1475640 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154901936 rs697727 A G 0.0052096 0.0022802 0.0219999 0.0223288 0.751288 0.643179 NA
23 154901964 rs697726 G A -0.0013953 0.0024114 0.5600000 0.5628493 0.347060 0.117616 NA
23 154902105 rs696316 G T 0.0051679 0.0022800 0.0230001 0.0234119 0.751224 0.636026 NA
23 154902889 rs697725 A T 0.0053783 0.0022793 0.0179999 0.0182923 0.750884 0.584106 NA
23 154903118 rs479770 G A 0.0052798 0.0022805 0.0210000 0.0206029 0.751346 0.643444 NA
23 154903224 rs480725 A T 0.0052805 0.0022805 0.0210000 0.0205870 0.751350 0.643444 NA
23 154903937 rs674707 G A 0.0052804 0.0022806 0.0210000 0.0205943 0.751363 0.643444 NA
23 154909055 rs473529 C G -0.0053588 0.0021485 0.0129999 0.0126226 0.305679 0.463046 NA
23 154918266 rs642043 C T -0.0055772 0.0021555 0.0097000 0.0096698 0.303509 0.478675 NA
23 154927581 rs644138 G A -0.0056043 0.0021559 0.0092999 0.0093366 0.303365 0.463576 NA

bcf preview

1   10177   rs1264289758    AC  A   .   PASS    AF=0.601646 ES:SE:LP:AF:ID  0.00323688:0.00292786:0.568636:0.601646:rs1264289758
1   10352   rs1557426776    TA  T   .   PASS    AF=0.606428 ES:SE:LP:AF:ID  0.00117545:0.00301122:0.154902:0.606428:rs1557426776
1   11008   rs575272151 C   G   .   PASS    AF=0.085879 ES:SE:LP:AF:ID  0.010567:0.00502777:1.4437:0.085879:rs575272151
1   11012   rs544419019 C   G   .   PASS    AF=0.085879 ES:SE:LP:AF:ID  0.010567:0.00502777:1.4437:0.085879:rs544419019
1   13110   rs540538026 G   A   .   PASS    AF=0.058602 ES:SE:LP:AF:ID  -0.00574132:0.00666763:0.408935:0.058602:rs540538026
1   13116   rs62635286  T   G   .   PASS    AF=0.189071 ES:SE:LP:AF:ID  -0.00199158:0.00394291:0.21467:0.189071:rs62635286
1   13118   rs62028691  A   G   .   PASS    AF=0.189071 ES:SE:LP:AF:ID  -0.00199158:0.00394291:0.21467:0.189071:rs62028691
1   13273   rs531730856 G   C   .   PASS    AF=0.134175 ES:SE:LP:AF:ID  0.00834392:0.0046075:1.1549:0.134175:rs531730856
1   14464   rs546169444 A   T   .   PASS    AF=0.156899 ES:SE:LP:AF:ID  -0.00240898:0.00420009:0.244125:0.156899:rs546169444
1   14599   rs707680    T   A   .   PASS    AF=0.191034 ES:SE:LP:AF:ID  -0.00750866:0.00382989:1.30103:0.191034:rs707680
1   14604   rs1418508701    A   G   .   PASS    AF=0.191034 ES:SE:LP:AF:ID  -0.00750866:0.00382989:1.30103:0.191034:rs1418508701
1   14930   rs6682385   A   G   .   PASS    AF=0.473851 ES:SE:LP:AF:ID  0.00105604:0.00296581:0.142668:0.473851:rs6682385
1   14933   rs199856693 G   A   .   PASS    AF=0.045051 ES:SE:LP:AF:ID  -0.000437241:0.00729697:0.0222764:0.045051:rs199856693
1   15211   rs3982632   T   G   .   PASS    AF=0.74123  ES:SE:LP:AF:ID  -0.00172196:0.0034301:0.207608:0.74123:rs3982632
1   15820   rs1316988498    G   T   .   PASS    AF=0.275129 ES:SE:LP:AF:ID  -0.00600037:0.00352124:1.05552:0.275129:rs1316988498
1   15903   rs557514207 GC  G   .   PASS    AF=0.581379 ES:SE:LP:AF:ID  -0.00506413:0.00290054:1.09151:0.581379:rs557514207
1   28590   rs1344649620    T   TTGG    .   PASS    AF=0.956576 ES:SE:LP:AF:ID  -0.00260217:0.00825743:0.124939:0.956576:rs1344649620
1   30923   rs1165072081    G   T   .   PASS    AF=0.910259 ES:SE:LP:AF:ID  -0.00528839:0.00548004:0.481486:0.910259:rs1165072081
1   47159   rs540662756 T   C   .   PASS    AF=0.062703 ES:SE:LP:AF:ID  0.00990579:0.00626235:0.958607:0.062703:rs540662756
1   49298   rs10399793  T   C   .   PASS    AF=0.623353 ES:SE:LP:AF:ID  0.00447045:0.00348723:0.69897:0.623353:rs10399793
1   49554   rs539322794 A   G   .   PASS    AF=0.093086 ES:SE:LP:AF:ID  0.00555844:0.00534879:0.522879:0.093086:rs539322794
1   51479   rs116400033 T   A   .   PASS    AF=0.213146 ES:SE:LP:AF:ID  -9.26962e-05:0.00372544:0.00877392:0.213146:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.154274 ES:SE:LP:AF:ID  -0.00255406:0.0041857:0.267606:0.154274:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.400998 ES:SE:LP:AF:ID  0.00117839:0.00344767:0.136677:0.400998:rs2462492
1   54712   rs573184866 TTTTC   T   .   PASS    AF=0.414722 ES:SE:LP:AF:ID  0.00412623:0.00273034:0.886057:0.414722:rs573184866
1   54716   rs1166278911    C   T   .   PASS    AF=0.417183 ES:SE:LP:AF:ID  0.000596914:0.00315092:0.0705811:0.417183:rs1166278911
1   55545   rs28396308  C   T   .   PASS    AF=0.253826 ES:SE:LP:AF:ID  0.00805666:0.00354612:1.63827:0.253826:rs28396308
1   58814   rs114420996 G   A   .   PASS    AF=0.090215 ES:SE:LP:AF:ID  0.00458779:0.00539273:0.408935:0.090215:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.088933 ES:SE:LP:AF:ID  0.00242523:0.00541952:0.187087:0.088933:rs62637815
1   60351   rs62637817  A   G   .   PASS    AF=0.081163 ES:SE:LP:AF:ID  0.000677298:0.00561812:0.0457575:0.081163:rs62637817
1   62777   rs3844233   A   T   .   PASS    AF=0.438166 ES:SE:LP:AF:ID  -0.00227876:0.0029958:0.346787:0.438166:rs3844233
1   63268   rs28664618  T   C   .   PASS    AF=0.382547 ES:SE:LP:AF:ID  0.00473673:0.00321723:0.853872:0.382547:rs28664618
1   63671   rs80011619  G   A   .   PASS    AF=0.158999 ES:SE:LP:AF:ID  -0.0042358:0.00409948:0.522879:0.158999:rs80011619
1   63735   rs61158452  C   CCTA    .   PASS    AF=0.684261 ES:SE:LP:AF:ID  9.993e-05:0.003193:0.00877392:0.684261:rs61158452
1   64931   rs62639104  G   A   .   PASS    AF=0.079801 ES:SE:LP:AF:ID  0.00122987:0.00568276:0.0809219:0.079801:rs62639104
1   68082   rs367789441 T   C   .   PASS    AF=0.070827 ES:SE:LP:AF:ID  -0.00733942:0.00577293:0.69897:0.070827:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.033029 ES:SE:LP:AF:ID  0.0120469:0.00868778:0.769551:0.033029:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.073948 ES:SE:LP:AF:ID  -0.00842309:0.00567768:0.853872:0.073948:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.750891 ES:SE:LP:AF:ID  -0.00396957:0.00361415:0.568636:0.750891:rs200676709
1   74790   rs13328700  C   G   .   PASS    AF=0.03412  ES:SE:LP:AF:ID  -0.00435813:0.00830441:0.221849:0.03412:rs13328700
1   74792   rs1335672253    G   A   .   PASS    AF=0.03412  ES:SE:LP:AF:ID  -0.00435813:0.00830441:0.221849:0.03412:rs1335672253
1   76838   rs563953605 T   G   .   PASS    AF=0.077214 ES:SE:LP:AF:ID  0.00121547:0.00579776:0.0809219:0.077214:rs563953605
1   76854   rs367666799 A   G   .   PASS    AF=0.07731  ES:SE:LP:AF:ID  0.00406243:0.00560929:0.327902:0.07731:rs367666799
1   77866   rs563593912 C   T   .   PASS    AF=0.077021 ES:SE:LP:AF:ID  0.00114503:0.00579934:0.0757207:0.077021:rs563593912
1   77874   rs62641297  G   A   .   PASS    AF=0.077021 ES:SE:LP:AF:ID  0.00114503:0.00579934:0.0757207:0.077021:rs62641297
1   81260   rs571136476 C   T   .   PASS    AF=0.041342 ES:SE:LP:AF:ID  0.0130241:0.00814144:0.958607:0.041342:rs571136476
1   81587   rs536406113 C   T   .   PASS    AF=0.061025 ES:SE:LP:AF:ID  -0.00646403:0.00614673:0.537602:0.061025:rs536406113
1   82163   rs139113303 G   A   .   PASS    AF=0.075292 ES:SE:LP:AF:ID  0.00480438:0.00568048:0.39794:0.075292:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.075324 ES:SE:LP:AF:ID  0.00447071:0.00567885:0.366532:0.075324:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.3529   ES:SE:LP:AF:ID  0.00166758:0.00324404:0.21467:0.3529:rs201754587