out (Required argument.) This parameter specifies the output file. miss This option can be used to change the code for missing values in the phenotype file file.pheno and covariate file v to the integer value of int. Each subject with at least one missing covariate will be dropped from the analysis. As for the phenotype file, the code -999 must be used to specify missing covariates (this code can be modified by using the -miss parameter).Ĭovariates are removed by replacing each phenotype by the residuals found after a multilinear regression between the phenotype and all of the covariates (with the intercept fit). The remaining lines specify the values of the covariates for the subjects (the subjects must be ordered in the same order as they are given in the phenotype file). The format of this file is the same as that for the phenotype file: it is space separated and the first line is a header specifying the names of the covariates. covar Specifies that covariates to be removed from the analysis are read from the file v. In this example phenotype file, the height and weight are given for 5 subjects, and the 5-th subject has a missing weight measurement. An example phenotype file is provided in the following listing: Missing values must be encoded by the code -999, or the code specified by the argument to the -miss parameter. ![]() Alternatively, if the subject IDs are present in the BGEN file, then they can be found using the qctool software, with the command qctool -g example.bgen -os example.sample (in some datasets, such as UK BIOBANK, the subject IDs are stripped from the BGEN files, in which case an accompanying SAMPLE file must be relied upon). If a SAMPLE file has been provided to accompany the BGEN files, then this order can be found by examining the SAMPLE file. The subjects must be presented in the same order that they are found in the BGEN file. This must be a space separated file, wherein the first line is a header line specifying the names of each phenotype as a space separated list, and the remaining lines specifying the values of the phenotypes for each subject. pheno (Required) The phenotypes for the subjects in the study must be specified by the file. See tools QCTOOL and BGENIX for more information about these sorts of files. ![]() It helps to have the BGEN file indexed (i.e produce a BGI file), which allows efficient PHEWAS and ranged based operations. bgen (Required) The BGEN file containing the genetic data for the subjects in the analysis must be specified by the file. If you wish to analyse just a single SNP you can select it using the –rsid option, for example: bgenie -bgen example.bgen -pheno example.pheno -out example.out -rsid rs573069994 If you wish to specify a range of SNPs specified by position (useful if you wish to split the genome up into multiple jobs) you can use the –range option, for example: bgenie -bgen example.bgen -pheno example.pheno -out example.out -range 22 20000000 21000000 A basic command to run GWAS on all the phenotypes is: bgenie -bgen example.bgen -pheno example.pheno -out example.out It has built in functionality to apply PCA or ICA (using the fastICA algorithm) to multiple phenotypes and use the resulting transformed phenotypes for testing via GWAS.īGENIE performs a linear association test between SNP/phenotype pairs in the provided data.For example, estimation of effect sizes of large numbers of SNPs can be carried out in parallel using matrix operations, and indexing of missing data values is used to allow for fast estimation of standard errors. BGENIE uses the Eigen matrix library and OpenMP to carry out as many of the linear algebra operations in parallel as possible.This feature facilitates very fast PHEWAS. It works with indexed BGEN files yielding fast access for any (group of) SNPs.This dataset consists of genetic data on ~500,000 individuals, ~93 Million autosomal variants and thousands of phenotypes. It was written for the analysis of the UK Biobank dataset (which is stored in the BGEN v1.2 file format).It takes BGEN files as input and avoids repeated decompression and conversion of these files when analyzing multiple continuous phenotypes. ![]()
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