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Question: merging multiple chromosomes in a single file
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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?

ADD COMMENTlink 10 months ago bigfoot • 0 • updated 10 months ago chrchang523 5.2k
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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.

ADD COMMENTlink 10 months ago chrchang523 5.2k

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