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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!

plink bgen qc snp genome

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.

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