How do I read BGEN format genotype data using BOLT-LMM?


Hi everyone,

I failed to read BGEN format imputed SNPs data ( ukb_imp_chr**_v3.bgen ) into BOLT-LMM software using csh.

According to the instruction, we can specify a list of whitespace-separated .bgen / .sample file pairs using the --bgenSampleFileList option. I used this option to load in genotype data and matched sample file, after submitting the job, an error info returned - Use exactly one of the --bfile, --bfilegz, or --fam, bim, bed input formats.

I tried --bfile option, but it gave me a new error - Unable to open file: /path/ukb_imp_chr**_v3.bgen.fam.

Could you please enlighten me how do I fix this problem? Really appreciate for any help.



BGEN format


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