Concatenation fails with "Non-concatenating --pmerge-list is under development"

[Arya Massarat]

Hello Chris,

I cannot figure out how to format my PGEN files to avoid this error:

Error: Non-concatenating --pmerge[-list] is under development.

What conditions must be satisfied for concatenation to proceed?

Here is a minimally reproducible example with a single variant. The variant is shared across the two files but there are different sets of samples in each file.

wget https://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_20251205.zip

unzip plink2_linux_x86_64_20251205.zip

for i in 1 2; do ./plink2 --out simple$i --vcf simple$i.vcf; done

./plink2 --pmerge-list <(ls simple{1,2}.pgen | sed 's/.pgen$//') --make-pgen --out simple

Thanks!

[Chris Chang]

"Concatenation" here means non-overlapping variant ranges.

You can use "bcftools merge" for non-overlapping samples.

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[Arya Massarat]

Ah, that makes much more sense! Thanks for the speedy response.

In that case, may I suggest a small change to the docs?

This statement:

(Only handles concatenation-like jobs for now.)

could instead be:

(We encapsulate the behavior of bcftools concat but not bcftools merge; --variant-inner-join and --merge-sids remain unimplemented for now.)