A VCF from this GWAS of Type 2 Diabetes https://doi.org/10.1038/s41588-018-0084-1. containing a subset of 10,000 variants

Source: R/vcf_sample.R

A VCF from this GWAS of Type 2 Diabetes https://doi.org/10.1038/s41588-018-0084-1. containing a subset of 10,000 variants

vcf_sample

Format

vcf_sample A CollapsedVCF

dim: 10000 1 rowRanges(vcf): GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER info(vcf): DataFrame with 1 column: AF info(header(vcf)): Number Type Description AF A Float Allele Frequency geno(vcf): List of length 9: ES, SE, LP, AF, SS, EZ, SI, NC, ID geno(header(vcf)): Number Type Description ES A Float Effect size estimate relative to the alternative allele SE A Float Standard error of effect size estimate LP A Float -log10 p-value for effect estimate AF A Float Alternate allele frequency in the association study SS A Integer Sample size used to estimate genetic effect EZ A Float Z-score provided if it was used to derive the EFFECT and SE fields SI A Float Accuracy score of summary data imputation NC A Integer Number of cases used to estimate genetic effect ID 1 String Study variant identifier