BOLT-LMM software has help information on the use of v3 imputation BGEN format genotype data.
9.1 UK Biobank v3 imputation release
The BGEN files in the UK Biobank v3 imputation release (7th March 2018) have the same format as the previous v2 release. These files are coded in the same BGEN sub-format (8-bit encoding, males coded as diploid) as the rest.
- Run BOLT-LMM on all files at once by using the --bgenSampleFileList option to specify a list of whitespace-separated .bgen / .sample file pairs. Note that you will need to --remove all samples not present in any of the BGEN files. (If BOLT-LMM detects missing samples, it will report an error and write a list of such samples for you to --remove.)
Could you please tell me what does "Run BOLT-LMM on all files at once" mean?
I coded like "--bgenSampleFileList=/path/ukb_imp_chr1_v3.bgen /path/ukb37334_imp_chr1_v3_s487324.sample \" to read in data, but it did not work. Anyone knows what's the problem?