keep allele order not working when converting 23andMe files

[Adam Willett]

Hello

Does the --keep-allele-order flag not work when converting from 23andMe files to Plink? 

I ran the following:

% ./plink --23file Adam_23andme.txt Willett Adam --keep-allele-order --out Adam_dna

PLINK v1.90b7.2 64-bit (11 Dec 2023)           www.cog-genomics.org/plink/1.9/

(C) 2005-2023 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to Adam_dna.log.

Options in effect:

  --23file Adam_23andme.txt Willett Adam

  --keep-allele-order

  --out Adam_dna

8192 MB RAM detected; reserving 4096 MB for main workspace.

--23file: Adam_dna.bed + Adam_dna.bim + Adam_dna.fam written.

Inferred sex: male.

Here are file comparisons of a short series of variants.

23andMe DNA file:

rs28456011 1 1567206 AG

rs7532034 1 1603163 TC

rs4074196 1 1611995 AG

rs4074197 1 1612111 TC

Bim file:

1 rs28456011 0 1567206 G A

1 rs7532034 0 1603163 C T

1 rs4074196 0 1611995 G A

1 rs4074197 0 1612111 C T

[Chris Chang]

—keep-allele-order does not change the behavior of the import commands.  Instead, it just prevents major alleles from being swapped to the A2 column later… but this has no effect in a single-sample dataset, since no swap occurs when both observed allele frequencies are 0.5.

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