Merge only bim files with plink

Question

[mgdrnl]

Hello

For the same dataset they provide a single BED and FAM files for all the chromosomes. However, the BIM files are split in chromosomes. I would like to generate the VCF file with the genotyping calls of all chromosomes but I need to merge the BIM files first. I generated a file "mergelist.txt" with the names of the bim files to merge and I tried the command below:

plink --bed name1 --fam name2 --merge-list mergelist.txt --make-bed --out merged

or:

plink --bed name1 --fam name2 --merge-list mergelist.txt --make-just-bim --out merged

I obtain the following error message:

Error: A full .bed + .bim + .fam fileset is required for this.

So I guess the problem is that in the "mergelist.txt" file there are only the names of the BIM without the corresponding BED and FAM. Do you know if it is possible to merge BIM files with a single BED and FAM?

Thank you in advance!

[chrchang523]

This question doesn't make sense: it is essentially not possible for a single .bed file to correspond to multiple .bim files. You need to get clarification from the source of these files re: how they are supposed to be read.