plink2 flag --alleleACGT is unrecognized.

Daniel Platt

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Jun 15, 2025, 7:03:03 PM6/15/25

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Plink2 did not recognize flag --alleleACGT., and suggested I try --help. The report from that message was:

plink2_mac_arm64_20250609 % plink2 --help --alleleACGT
PLINK v2.0.0-a.6.16 M1 (9 Jun 2025) cog-genomics.org/plink/2.0/
(C) 2005-2025 Shaun Purcell, Christopher Chang GNU General Public License v3

No help entry for '--alleleACGT'.

However, your documentation (https://www.cog-genomics.org/plink/2.0/data#export) states:

--allele1234 interprets and/or recodes A/C/G/T alleles in the input as 1/2/3/4, while --alleleACGT does the reverse. With the 'multichar' modifier, these will translate multi-character alleles as well, e.g. '--allele1234 multichar' converts 'TT' to '44'.

This is actually a useful flag since the David Reich aDNA datasets converts to .ped with allele1234 formatting (ugghhh).

Thx!

Christopher Chang

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Jun 15, 2025, 7:14:00 PM6/15/25

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In the command summary, "--allele1234" is in red text. From "Interpreting our flag usage summaries" (https://www.cog-genomics.org/plink/2.0/general_usage#flag_usage ), there is:

If parts of our current implementation are known or strongly suspected to be incomplete, that is signaled with red text.

But thanks for noting that this flag would be helpful; I'll implement it in an upcoming development build.

Christopher Chang

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Jun 27, 2025, 8:33:44 PM6/27/25

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A build with --allele1234/--alleleACGT, as well as direct --eigfile / "--export eig" conversion to/from PACKEDANCESTRYMAP filesets, has been posted; let me know if you run into any problems with it.

On Sunday, June 15, 2025 at 4:03:03 PM UTC-7 daniel...@gmail.com wrote:

7X

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Jul 9, 2025, 7:55:13 AM7/9/25

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Hi Chris,

This flag --allele1234 is still not working with the latest build Alpha 6.20 (7 Jul).

Here is the error log.

Error: Unrecongnized flag ('--allele1234').

For more info, try "plink2 --help <flag name>" or "plink2 --help | more".

Thanks in advance.

Chris Chang

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Jul 9, 2025, 9:05:03 AM7/9/25

to 7X, plink2-users

You need to use the development build.

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