Sidebar

IEU GWAS information

Trait: Waist-to-hip ratio.

name	value
id	ieu-a-83
pmid	25673412
year	2015
mr	1
note	Adjusted for BMI
trait	Waist-to-hip ratio
category	Risk factor
subcategory	Anthropometric
population	European
sex	Males
ncase	NULL
ncontrol	NULL
sample_size	93478
nsnp	2146137
sd	0.0741601501
priority	14
author	Shungin D
group_name	public
access	public
build	HG19/GRCh37

Report information

name	value
gwas_id	ieu-a-83
bcf_file	ieu-a-83.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 01:42 BST
build_version	run_igd-8f4f4c9-2020-05-09

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-a-83,TotalVariants=2145319,VariantsNotRead=0,HarmonisedVariants=2145319,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-83/ieu-a-83_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T08:08:40.676183",
    "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-83/ieu-a-83.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-83/ieu-a-83_data.vcf.gz; Date=Tue Feb  4 10:05:43 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-83/ieu-a-83.vcf.gz; Date=Sun May 10 01:34:29 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-83/ieu-a-83.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-83/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 19:40:21 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-83/ieu-a-83.vcf.gz ...
Read summary statistics for 2145319 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, 1027851 SNPs remain.
After merging with regression SNP LD, 1027851 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1224 (0.0101)
Lambda GC: 1.0265
Mean Chi^2: 1.0495
Intercept: 0.9094 (0.0073)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb  4 19:40:48 2020
Total time elapsed: 26.96s

QC metrics

Metrics

{
    "af_correlation": 0.9052,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -3.8589e-06,
    "n": 93480,
    "n_snps": 2145319,
    "n_clumped_hits": 6,
    "n_p_sig": 95,
    "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": 7311,
    "n_miss_AF_reference": 16719,
    "n_est": 95179.047,
    "ratio_se_n": 1.009,
    "mean_diff": 2.0038e-06,
    "ratio_diff": 3.2185,
    "sd_y_est1": 1.3898,
    "sd_y_est2": 1.4024,
    "r2_sum1": 0.0029,
    "r2_sum2": 0.0015,
    "r2_sum3": 0.0015,
    "r2_sum4": 0.0024,
    "ldsc_nsnp_merge_refpanel_ld": 1027851,
    "ldsc_nsnp_merge_regression_ld": 1027851,
    "ldsc_observed_scale_h2_beta": 0.1224,
    "ldsc_observed_scale_h2_se": 0.0101,
    "ldsc_intercept_beta": 0.9094,
    "ldsc_intercept_se": 0.0073,
    "ldsc_lambda_gc": 1.0265,
    "ldsc_mean_chisq": 1.0495,
    "ldsc_ratio": -1.8303
}

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	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	numeric.mean	numeric.sd	numeric.p0	numeric.p25	numeric.p50	numeric.p75	numeric.p100	numeric.hist
character	ID	0	1.0000000	3	42	0	2145319	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	8.514304e+00	5.615595e+00	1.0000e+00	4.000000e+00	8.000000e+00	1.200000e+01	2.300000e+01	▇▅▅▂▂
numeric	POS	0	1.0000000	NA	NA	NA	NA	NA	7.900599e+07	5.538669e+07	1.3034e+04	3.308772e+07	7.051721e+07	1.142307e+08	2.491747e+08	▇▇▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	-3.900000e-06	9.607500e-03	-1.1000e-01	-5.700000e-03	0.000000e+00	5.600000e-03	1.200000e-01	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	8.919800e-03	3.306300e-03	4.9000e-03	6.800000e-03	7.600000e-03	9.900000e-03	5.300000e-02	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.956467e-01	2.910394e-01	0.0000e+00	2.399999e-01	4.899999e-01	7.499995e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.956387e-01	2.909210e-01	0.0000e+00	2.433450e-01	4.942630e-01	7.478856e-01	1.000000e+00	▇▇▇▇▇
numeric	AF	7311	0.9965921	NA	NA	NA	NA	NA	3.754182e-01	2.623567e-01	8.3000e-03	1.500000e-01	3.167000e-01	5.750000e-01	9.917000e-01	▇▆▅▃▂
numeric	AF_reference	16719	0.9922068	NA	NA	NA	NA	NA	3.762089e-01	2.462155e-01	1.9970e-04	1.691290e-01	3.220850e-01	5.567090e-01	9.996010e-01	▇▇▅▃▂
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	5.697486e+04	7.150272e+03	5.0000e+04	5.594700e+04	5.644300e+04	5.652200e+04	9.348000e+04	▇▁▁▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	785050	rs2905062	G	A	0.0010	0.0092	0.9100000	0.9134439	NA	0.626997	58652
1	1003629	rs4075116	C	T	0.0090	0.0082	0.2700001	0.2723962	0.73730	0.720647	53615
1	1017170	rs3766193	C	G	0.0110	0.0075	0.1299999	0.1424668	0.56670	0.575479	54154
1	1017197	rs3766192	C	T	0.0120	0.0072	0.0879995	0.0955807	0.57630	0.511182	54437
1	1018562	rs9442371	C	T	0.0130	0.0071	0.0759994	0.0671026	0.59170	0.530152	54480
1	1018704	rs9442372	A	G	0.0100	0.0071	0.1499999	0.1589977	0.60170	0.611022	54487
1	1021415	rs3737728	A	G	0.0090	0.0077	0.2399999	0.2424717	0.71670	0.812700	54763
1	1021695	rs9442398	A	G	0.0110	0.0081	0.1600000	0.1744558	0.72500	0.727236	54638
1	1097335	rs9442385	T	G	-0.0051	0.0130	0.6999999	0.6948309	0.94167	0.834665	51620
1	1099342	rs9660710	A	C	-0.0017	0.0130	0.8900000	0.8959579	0.94068	0.829872	54300

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
22	51151350	rs6009951	C	T	0.0110	0.0071	0.1100001	0.1213106	0.4000	0.5559110	55474
22	51151724	rs6010061	C	T	0.0120	0.0072	0.0980009	0.0955807	0.3833	0.6098240	55304
22	51158017	rs6010065	G	C	0.0120	0.0068	0.0879995	0.0776132	0.4417	0.5475240	55181
22	51163138	rs715586	C	T	0.0018	0.0076	0.8100000	0.8127793	0.1500	0.0902556	85516
22	51165664	rs8137951	G	A	0.0034	0.0055	0.5400003	0.5364555	0.2750	0.4063500	91425
22	51178090	rs2285395	G	A	0.0150	0.0110	0.1600000	0.1726820	0.0667	0.0666933	87344
23	35921591	rs2204667	C	G	0.0160	0.0088	0.0759994	0.0690363	0.1667	NA	56471
23	51666786	rs14115	A	G	0.0098	0.0140	0.5000000	0.4839273	0.0250	NA	51110
23	70163799	rs1626496	A	C	0.0110	0.0130	0.3900004	0.3974669	0.0750	NA	56484
23	118495837	rs12882977	G	A	0.0097	0.0065	0.1400000	0.1356185	0.5167	0.2307280	56406

bcf preview

1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.001:0.0092:0.0409586:58652:rs2905062
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.009:0.0082:0.568636:0.7373:53615:rs4075116
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.011:0.0075:0.886057:0.5667:54154:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.012:0.0072:1.05552:0.5763:54437:rs3766192
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   0.013:0.0071:1.11919:0.5917:54480:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   0.01:0.0071:0.823909:0.6017:54487:rs9442372
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   0.009:0.0077:0.619789:0.7167:54763:rs3737728
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.011:0.0081:0.79588:0.725:54638:rs9442398
1   1097335 rs9442385   T   G   .   PASS    AF=0.94167  ES:SE:LP:AF:SS:ID   -0.0051:0.013:0.154902:0.94167:51620:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.94068  ES:SE:LP:AF:SS:ID   -0.0017:0.013:0.05061:0.94068:54300:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.95833  ES:SE:LP:AF:SS:ID   0.019:0.018:0.552842:0.95833:54064:rs1891905
1   1124663 rs6684820   G   A   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0026:0.0083:0.124939:0.2667:53843:rs6684820
1   1125553 rs10907174  A   T   .   PASS    AF=0.225    ES:SE:LP:AF:SS:ID   0.008:0.0087:0.443698:0.225:53741:rs10907174
1   1130727 rs10907175  A   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0062:0.012:0.21467:0.1:54863:rs10907175
1   1135242 rs9729550   A   C   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   0.0022:0.0081:0.102373:0.275:53774:rs9729550
1   1138913 rs3819001   T   C   .   PASS    AF=0.0431   ES:SE:LP:AF:SS:ID   -0.017:0.018:0.455932:0.0431:52121:rs3819001
1   1140435 rs1815606   G   T   .   PASS    AF=0.3103   ES:SE:LP:AF:SS:ID   -0.0033:0.0062:0.229148:0.3103:72161:rs1815606
1   1143657 rs3753348   C   G   .   PASS    AF=0.03333  ES:SE:LP:AF:SS:ID   -0.015:0.02:0.337242:0.03333:52119:rs3753348
1   1152631 rs11721 C   A   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.016:0.013:0.69897:0.08333:53056:rs11721
1   1158277 rs3813199   G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0085:0.012:0.327902:0.1:54766:rs3813199
1   1162435 rs3766186   C   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0096:0.012:0.376751:0.1:54753:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.0001:0.01:0.00436481:0.15:54714:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.05172  ES:SE:LP:AF:SS:ID   -0.0084:0.016:0.221849:0.05172:51440:rs11260562
1   1176597 rs6675798   T   C   .   PASS    AF=0.1083   ES:SE:LP:AF:SS:ID   0.018:0.012:0.79588:0.1083:52003:rs6675798
1   1181751 rs6603783   T   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.016:0.013:0.69897:0.1:53070:rs6603783
1   1192515 rs7524470   A   G   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   -0.012:0.019:0.29243:0.05833:50050:rs7524470
1   1194804 rs11804831  T   C   .   PASS    AF=0.2083   ES:SE:LP:AF:SS:ID   0.0035:0.0093:0.148742:0.2083:54645:rs11804831
1   1198618 rs12563338  T   A   .   PASS    AF=0.04167  ES:SE:LP:AF:SS:ID   -0.022:0.019:0.60206:0.04167:53299:rs12563338
1   1206343 rs6667923   C   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   -0.0086:0.018:0.19382:0.05833:54459:rs6667923
1   1206619 rs6668223   C   A   .   PASS    AF=0.0339   ES:SE:LP:AF:SS:ID   -0.0059:0.021:0.107905:0.0339:54246:rs6668223
1   1211292 rs6685064   C   T   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.019:0.013:0.853872:0.1:53318:rs6685064
1   1474304 rs1571150   C   A   .   PASS    AF=0.3  ES:SE:LP:AF:SS:ID   -0.0056:0.007:0.376751:0.3:55982:rs1571150
1   1478153 rs3766180   T   C   .   PASS    AF=0.2417   ES:SE:LP:AF:SS:ID   -0.0062:0.0073:0.39794:0.2417:56404:rs3766180
1   1478180 rs3766178   T   C   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   -0.0068:0.0073:0.455932:0.2667:56279:rs3766178
1   1481348 rs3766177   T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.0041:0.0079:0.221849:55307:rs3766177
1   1483010 rs7517401   G   A   .   PASS    AF=0.2833   ES:SE:LP:AF:SS:ID   -0.0053:0.0073:0.327902:0.2833:55848:rs7517401
1   1486834 rs3128342   C   A   .   PASS    AF=0.3333   ES:SE:LP:AF:SS:ID   -0.0036:0.0074:0.200659:0.3333:50812:rs3128342
1   1489670 rs7531530   C   T   .   PASS    AF=0.25 ES:SE:LP:AF:SS:ID   -0.0044:0.0075:0.251812:0.25:55903:rs7531530
1   1489928 rs7366884   T   C   .   PASS    AF=0.25 ES:SE:LP:AF:SS:ID   -0.0046:0.0077:0.259637:0.25:55899:rs7366884
1   1497201 rs3766169   A   C   .   PASS    AF=0.2458   ES:SE:LP:AF:SS:ID   -0.0059:0.0072:0.387216:0.2458:56447:rs3766169
1   1499298 rs9439468   A   G   .   PASS    AF=0.3103   ES:SE:LP:AF:SS:ID   -0.0052:0.0069:0.346787:0.3103:56372:rs9439468
1   1500941 rs6603791   A   G   .   PASS    AF=0.3  ES:SE:LP:AF:SS:ID   -0.0049:0.0069:0.318759:0.3:56380:rs6603791
1   1501064 rs6656541   T   G   .   PASS    AF=0.3  ES:SE:LP:AF:SS:ID   -0.0049:0.007:0.318759:0.3:56365:rs6656541
1   1505255 rs6603793   C   T   .   PASS    AF=0.3  ES:SE:LP:AF:SS:ID   -0.0049:0.0069:0.318759:0.3:56340:rs6603793
1   1509034 rs7520996   T   C   .   PASS    AF=0.2797   ES:SE:LP:AF:SS:ID   -0.0039:0.0071:0.236572:0.2797:55965:rs7520996
1   1510801 rs7519837   C   T   .   PASS    AF=0.2917   ES:SE:LP:AF:SS:ID   -0.0046:0.0071:0.283997:0.2917:55986:rs7519837
1   1706136 rs6603811   T   C   .   PASS    AF=0.97458  ES:SE:LP:AF:SS:ID   -0.014:0.012:0.638272:0.97458:78632:rs6603811
1   1706160 rs7531583   A   G   .   PASS    AF=0.7833   ES:SE:LP:AF:SS:ID   -0.0056:0.0059:0.468521:0.7833:91239:rs7531583
1   1708801 rs12044597  A   G   .   PASS    AF=0.5169   ES:SE:LP:AF:SS:ID   -0.0072:0.005:0.823909:0.5169:91254:rs12044597
1   1721479 rs2272908   C   T   .   PASS    AF=0.5167   ES:SE:LP:AF:SS:ID   -0.0042:0.0065:0.283997:0.5167:56511:rs2272908