I am using Rstudio workbench within UK Biobank RAP. I have successfully imported a phenotype file into Rstudio workbench, and now I need to load in genotype data from within my project (from bulk>genotype results>genotype calls and bulk>imputation>UKB imputation from genotype). I?m not quite sure how to do this though as I don?t know what the different file types for each chromosome mean (.bim, .bed, .bfam, .bgen, .bgen.bi, .mfi.txt, .sample), or whether they have EIDs which will allow me to merge the genotype data with the phenotype data. Can you point me to any resources which explain the genotype data files more clearly or the process for doing these analyses in Rstudio workbench/RAP?
There are video tutorials on GWAS and Rstudio workbench on RAP here that could be useful.
There are different type of genomics format on RAP. Multiple format are provided for convenient purpose. Roughly, there are vcf (e.g. pvcf), PLINK (bed, bim, fam), BGEN (bgen, bgen.bgi). These are formal format name that you can search to read more about their spec. For example, you can find PLINK document here. In most basic use case, you would only need one or two of them for your work.
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There are video tutorials on GWAS and Rstudio workbench on RAP here that could be useful.
There are different type of genomics format on RAP. Multiple format are provided for convenient purpose. Roughly, there are vcf (e.g. pvcf), PLINK (bed, bim, fam), BGEN (bgen, bgen.bgi). These are formal format name that you can search to read more about their spec. For example, you can find PLINK document here. In most basic use case, you would only need one or two of them for your work.
There is a tutorial that community member {@005t0000008C83jAAC}? made as well. https://community.dnanexus.com/s/question/0D5t00000416OTeCAM/performing-gwas-on-rap-using-dx-toolkit-and-swissarmyknife You may find it useful.
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