merge-list in plink1 vs pmerge-list in plink2

[Y P]

Hi,

I have been using plink2 --make-bed to generate some plink 1 format files (.bed .bim .fam). I am sure they are with the same sample set and non overlap variants. Is there a difference using plink2's pmerge-list vs plink1's merge-list to merge those plink files?

I have been using plink2 for my pipeline but it seems pmerge-list is relatively new and has some difference than the merge-list in plink1. I just want to make sure the merge files has no compatibility issue.

Many thanks!

[Christopher Chang]

The most important difference right now is that --pmerge-list only handles concatenation jobs (e.g. merging a split-by-chromosome dataset) for now.  If there are any variants shared between multiple input files, --pmerge-list doesn't work yet.

For those concatenation jobs, --pmerge-list is more likely to do what you want than plink1 --merge-list: variants are matched by position and ID, rather than just ID, so missing-ID variants aren't a problem.