bgen files split by chromosome

Question

[ravibot]

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!

[chrchang523]

For now, you can use plink2 to convert the per-chromosome .bgen files to BCF, use bcftools concat to 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.