https://medlineplus.gov/genetics/understanding/howgeneswork/genelocation/

Please go through this. It may help.

Hi Marva,

Add CHROMOSOMELABEL and POSITIONLABEL for each input file in the Metal command file. I also recommend considering the random-effects model using Random-Metal or GWAMA software to account for heterogeneity.

Good luck.

Mehdi Esmaeili-Fard Thank you for your answer.

Do you mean Add them as custom variables as in the link ? https://genome.sph.umich.edu/wiki/METAL_Documentation#Custom_Variables

If so that doesn't work because it will add the chr number across all input files.

It's not needed to define custom variables. Both CHROMOSOMELABEL and POSITIONLABEL are predefined commands/keywords in Metal. Just use them for each input. I've forgotten to say that you need to add "TRACKPOSITIONS ON" at the top of your command file.