Sidebar

IEU GWAS information

Trait: Weight change during worst episode of depression: Stayed about the same or was on a diet.

name	value
id	ukb-d-20536_0
trait	Weight change during worst episode of depression: Stayed about the same or was on a diet
category	Binary
ncase	22981
ncontrol	33590
sample_size	56571
sex	Males and females
population	European
group_name	public
access	public
build	HG19/GRCh37
author	Neale lab
year	2018
mr	1
nsnp	13556976

Report information

name	value
gwas_id	ukb-d-20536_0
bcf_file	ukb-d-20536_0.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 02:30 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=ukb-d-20536_0,TotalVariants=13556975,VariantsNotRead=0,HarmonisedVariants=13556975,VariantsNotHarmonised=0,SwitchedAlleles=229,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-20536_0/ukb-d-20536_0_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T15:14:49.566434",
    "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-20536_0/ukb-d-20536_0.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20536_0/ukb-d-20536_0_data.vcf.gz; Date=Mon Nov 25 15:55:00 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-20536_0/ukb-d-20536_0.vcf.gz; Date=Sun May 10 01:58:12 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-20536_0/ukb-d-20536_0.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-20536_0/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 16:38:35 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20536_0/ukb-d-20536_0.vcf.gz ...
Read summary statistics for 13556975 SNPs.
Dropped 12670 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, 1283502 SNPs remain.
After merging with regression SNP LD, 1283502 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0625 (0.0082)
Lambda GC: 1.0468
Mean Chi^2: 1.0532
Intercept: 0.9836 (0.0064)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 16:41:26 2019
Total time elapsed: 2.0m:51.0s

QC metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0361,
    "mean_EFFECT": 0,
    "n": 56571,
    "n_snps": 13556975,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1250797,
    "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": 560985,
    "n_est": 56707.6058,
    "ratio_se_n": 1.0012,
    "mean_diff": 0,
    "ratio_diff": 6.6843,
    "sd_y_est1": 0.4771,
    "sd_y_est2": 0.4777,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283502,
    "ldsc_nsnp_merge_regression_ld": 1283502,
    "ldsc_observed_scale_h2_beta": 0.0625,
    "ldsc_observed_scale_h2_se": 0.0082,
    "ldsc_intercept_beta": 0.9836,
    "ldsc_intercept_se": 0.0064,
    "ldsc_lambda_gc": 1.0468,
    "ldsc_mean_chisq": 1.0532,
    "ldsc_ratio": -0.3083
}

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	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	94	0	13544969	0	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.0000000	1	100	0	57030	0	NA	NA	NA	NA	NA	NA	NA	NA
character	ALT	0	1.0000000	1	342	0	33322	0	NA	NA	NA	NA	NA	NA	NA	NA
numeric	CHROM	0	1.0000000	NA	NA	NA	NA	NA	9.051455e+00	6.185029e+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	7.902549e+07	5.591643e+07	3.02000e+02	3.292765e+07	7.013848e+07	1.148599e+08	2.492309e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	1.370000e-05	1.653710e-02	-2.02664e-01	-4.455700e-03	-2.360000e-05	4.432700e-03	2.028330e-01	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	1.185230e-02	1.141540e-02	2.41720e-03	3.390300e-03	6.229900e-03	1.701410e-02	5.830810e-02	▇▂▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.941716e-01	2.899421e-01	1.00000e-07	2.419079e-01	4.923659e-01	7.448246e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.941687e-01	2.899438e-01	1.00000e-07	2.419028e-01	4.923631e-01	7.448239e-01	1.000000e+00	▇▇▇▇▇
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	1.911924e-01	2.544963e-01	1.00000e-03	7.536800e-03	6.048150e-02	2.961090e-01	9.990000e-01	▇▂▁▁▁
numeric	AF_reference	560985	0.9586202	NA	NA	NA	NA	NA	1.966128e-01	2.471591e-01	0.00000e+00	5.790700e-03	8.466450e-02	3.087060e-01	1.000000e+00	▇▂▁▁▁
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	5.657100e+04	0.000000e+00	5.65710e+04	5.657100e+04	5.657100e+04	5.657100e+04	5.657100e+04	▁▁▇▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	692794	rs530212009	CA	C	-0.0059244	0.0049330	0.2297698	0.2297659	0.1120070	0.1894970	56571
1	693731	rs12238997	A	G	-0.0046384	0.0046662	0.3202057	0.3202023	0.1168710	0.1417730	56571
1	707522	rs371890604	G	C	-0.0039008	0.0052399	0.4566054	0.4566010	0.0983231	0.1293930	56571
1	717587	rs144155419	G	A	-0.0202286	0.0124996	0.1055949	0.1055894	0.0158084	0.0045926	56571
1	723329	rs189787166	A	T	0.0496385	0.0355562	0.1627020	0.1626972	0.0018800	0.0003994	56571
1	730087	rs148120343	T	C	0.0037502	0.0064980	0.5638531	0.5638510	0.0569925	0.0127796	56571
1	731718	rs142557973	T	C	-0.0055550	0.0044273	0.2095820	0.2095769	0.1228370	0.1543530	56571
1	732032	rs61770163	A	C	-0.0060753	0.0047168	0.1977420	0.1977366	0.1222970	0.1555510	56571
1	734349	rs141242758	T	C	-0.0059226	0.0044293	0.1811799	0.1811743	0.1221100	0.1525560	56571
1	740284	rs61770167	C	T	-0.0403195	0.0198302	0.0420339	0.0420286	0.0060746	0.0023962	56571

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
23	154923311	rs141127553	C	T	0.0042094	0.0053668	0.4328436	0.4328404	0.0559256	0.0309934	56571
23	154923374	rs111332691	T	A	-0.0008739	0.0059356	0.8829551	0.8829542	0.0437061	0.0116556	56571
23	154925045	rs509981	C	T	0.0026734	0.0028208	0.3432567	0.3432520	0.2456330	0.3634440	56571
23	154925895	rs538470	C	T	0.0024433	0.0028845	0.3969831	0.3969780	0.2420240	0.3634440	56571
23	154927581	rs644138	G	A	0.0034038	0.0026531	0.1995019	0.1994955	0.3019940	0.4635760	56571
23	154929412	rs557132	C	T	0.0027727	0.0028215	0.3257452	0.3257409	0.2455120	0.3568210	56571
23	154929637	rs35185538	CT	C	0.0034684	0.0029491	0.2395648	0.2395601	0.2288990	0.3011920	56571
23	154929952	rs4012982	CAA	C	0.0035154	0.0029738	0.2371598	0.2371547	0.2391570	0.3165560	56571
23	154930230	rs781880	A	G	0.0027404	0.0028211	0.3313470	0.3313434	0.2458300	0.3618540	56571
23	154930487	rs781879	T	A	-0.0005952	0.0096268	0.9506980	0.9506974	0.0194161	0.1263580	56571

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.112007 ES:SE:LP:AF:SS:ID   -0.00592437:0.00493302:0.638707:0.112007:56571:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116871 ES:SE:LP:AF:SS:ID   -0.00463839:0.00466619:0.494571:0.116871:56571:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0983231    ES:SE:LP:AF:SS:ID   -0.00390085:0.00523987:0.340459:0.0983231:56571:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0158084    ES:SE:LP:AF:SS:ID   -0.0202286:0.0124996:0.976357:0.0158084:56571:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00187996   ES:SE:LP:AF:SS:ID   0.0496385:0.0355562:0.788607:0.00187996:56571:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0569925    ES:SE:LP:AF:SS:ID   0.00375022:0.00649804:0.248834:0.0569925:56571:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122837 ES:SE:LP:AF:SS:ID   -0.00555504:0.00442728:0.678646:0.122837:56571:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122297 ES:SE:LP:AF:SS:ID   -0.00607534:0.00471678:0.703901:0.122297:56571:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12211  ES:SE:LP:AF:SS:ID   -0.00592263:0.0044293:0.74189:0.12211:56571:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00607462   ES:SE:LP:AF:SS:ID   -0.0403195:0.0198302:1.3764:0.00607462:56571:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00187725   ES:SE:LP:AF:SS:ID   0.0633924:0.0383435:1.00753:0.00187725:56571:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869034 ES:SE:LP:AF:SS:ID   0.00631903:0.00436619:0.830243:0.869034:56571:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00152552   ES:SE:LP:AF:SS:ID   0.0461585:0.0396191:0.612608:0.00152552:56571:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.123945 ES:SE:LP:AF:SS:ID   -0.00637252:0.00432367:0.852253:0.123945:56571:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143307 ES:SE:LP:AF:SS:ID   -0.00566276:0.00428071:0.730746:0.143307:56571:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12403  ES:SE:LP:AF:SS:ID   -0.00626723:0.00431811:0.833632:0.12403:56571:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869798 ES:SE:LP:AF:SS:ID   0.00787045:0.00421055:1.21044:0.869798:56571:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874432 ES:SE:LP:AF:SS:ID   0.00631344:0.00427792:0.853878:0.874432:56571:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129654 ES:SE:LP:AF:SS:ID   -0.00801485:0.00422068:1.23975:0.129654:56571:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0366265    ES:SE:LP:AF:SS:ID   -0.00512344:0.00766224:0.297816:0.0366265:56571:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.8694   ES:SE:LP:AF:SS:ID   0.00788211:0.00420586:1.21521:0.8694:56571:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.86946  ES:SE:LP:AF:SS:ID   0.00791877:0.00420676:1.22339:0.86946:56571:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869403 ES:SE:LP:AF:SS:ID   0.00788047:0.00420572:1.21488:0.869403:56571:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00495789   ES:SE:LP:AF:SS:ID   -0.0173167:0.0219215:0.36697:0.00495789:56571:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00492638   ES:SE:LP:AF:SS:ID   -0.0176165:0.0219692:0.37404:0.00492638:56571:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00576142   ES:SE:LP:AF:SS:ID   -0.00502137:0.0207012:0.0924038:0.00576142:56571:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869451 ES:SE:LP:AF:SS:ID   0.0082679:0.00419859:1.31039:0.869451:56571:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.127054 ES:SE:LP:AF:SS:ID   -0.00859067:0.00428285:1.34796:0.127054:56571:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.868952 ES:SE:LP:AF:SS:ID   0.00819824:0.00418734:1.29886:0.868952:56571:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868377 ES:SE:LP:AF:SS:ID   0.00771225:0.00418487:1.18475:0.868377:56571:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.86916  ES:SE:LP:AF:SS:ID   0.00821056:0.00419154:1.29985:0.86916:56571:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869166 ES:SE:LP:AF:SS:ID   0.00820884:0.00419182:1.2993:0.869166:56571:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.86917  ES:SE:LP:AF:SS:ID   0.00820748:0.00419186:1.29895:0.86917:56571:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869567 ES:SE:LP:AF:SS:ID   0.00812542:0.00420209:1.27442:0.869567:56571:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0998903    ES:SE:LP:AF:SS:ID   -0.00703347:0.00487444:0.82668:0.0998903:56571:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00671909   ES:SE:LP:AF:SS:ID   -0.0186981:0.0185706:0.503063:0.00671909:56571:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87357  ES:SE:LP:AF:SS:ID   0.00673171:0.00426636:0.9408:0.87357:56571:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862977 ES:SE:LP:AF:SS:ID   0.00745768:0.00418376:1.12687:0.862977:56571:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868296 ES:SE:LP:AF:SS:ID   0.00768411:0.00422583:1.16107:0.868296:56571:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865477 ES:SE:LP:AF:SS:ID   0.00816362:0.00422987:1.27073:0.865477:56571:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.100288 ES:SE:LP:AF:SS:ID   -0.00831415:0.00503722:1.00508:0.100288:56571:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870571 ES:SE:LP:AF:SS:ID   0.00746523:0.00427568:1.09248:0.870571:56571:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870571 ES:SE:LP:AF:SS:ID   0.00746631:0.00427567:1.09272:0.870571:56571:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870568 ES:SE:LP:AF:SS:ID   0.00746663:0.00427568:1.09278:0.870568:56571:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870876 ES:SE:LP:AF:SS:ID   0.00707288:0.00427693:1.00794:0.870876:56571:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126626 ES:SE:LP:AF:SS:ID   -0.00779663:0.00427868:1.16476:0.126626:56571:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106451 ES:SE:LP:AF:SS:ID   -0.00454611:0.00465252:0.483451:0.106451:56571:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85426  ES:SE:LP:AF:SS:ID   0.00713312:0.00418222:1.05506:0.85426:56571:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00178176   ES:SE:LP:AF:SS:ID   0.0429243:0.035778:0.63781:0.00178176:56571:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.837605 ES:SE:LP:AF:SS:ID   0.000342775:0.00413736:0.0296661:0.837605:56571:rs376645387