bgen files split by chromosome
Hello,
I currently have bgen files split by chromosome and would like to combine them into one file so I could run QC in plink. Does anyone have any suggestions on how to do this?
Thanks in advance!
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For now, you can use plink2 to convert the per-chromosome .bgen files to BCF, use
bcftools concatto concatenate the BCFs, and then feed that concatenated BCF to plink2.plink2 will soon have a --pmerge-list command that'll get the job done faster.