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merging multiple chromosomes in a single file

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?

plink gwas prs snp
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updated by chrchang523 chrchang523 • written by bigfoot • bigfoot

1 answer

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.

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written by chrchang523 chrchang523

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