merging multiple chromosomes in a single file

Question

[bigfoot]

I have multiple separated chromosomes (1-22+X) in .pgen .bim .fam extensions (PLINK2 binary). How could I merge all chromosomes in a single .pgen .bim .fam file?

Answer 1

[chrchang523]

This isn't built into plink2 yet (which is why it is still in alpha testing; --pmerge is the last major function that needs to be completed before beta testing can begin).

A reasonable workaround for now is to export to VCF, use "bcftools concat", and then re-import.