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Re-joining sample ID's and snp information from bgen files for analysis in R

Hey, I have some UKBB data that I have pulled a set of snps from and need to analyse in R. Due to this, i need to get the sample ID's back connected to the genotype information so that i can merge it with the phenotype file later on for analysis. Can someone point me in the general direction of doing that? Thank you so much.

snp r snp
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written by nreid • nreid

2 answers

You can try to convert the BGEN file into a VCF or uncompressed GEN fille and extract the SNPs / samples at the same time using QCTools developed by BGEN's author.

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written by Sam Sam

I've done this, but it appears that there are no sample identifiers in the VCF file so that the data is essentially useless in my analysis since i need to merge with phenotype data. for example when using snpStats package on a pedfile i usually get the snp of interest coupled to the patient identifier and 0,1,2 for null/het/homo at that snp which was pulled. For whatever reason i cant convert to pedfiles.

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written by nreid • nreid

EDIT: I solved my issue using the vcfR package and a little more patience reading things. reading the filtered vcf into R using: test= read.vcfR("file/path/here") then extracting with tidytest = extract_gt_tidy(x=test) yielded the results I was looking for.

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written by nreid • nreid

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