Merging snippy core output

Dear all,

I need to run snippy-core on a large set of samples (around 1000). Due to the large amount of space it takes, I can’t run snippy and the snippy-core on all of them at one in the Galaxy server so, is it ok if I run snippy/snippy-core in chunks and then merge the final snippy-core output into one big file?
My main concern is that I don’t actually know if the SNP positions in separate analyses are the same so the final output wouldn’t be comparable. I would obviously use the same reference.
Or is it better to merge every snippy output and then perform a single snippy-core?

Thank you!