Comparing SNP coordinates from alignments to different reference genomes

Question

[shpak.max]

I have a list of SNP coordinates of interest based on a study that used Drosophila reference genome 5.18. I would like to compare these to some data that we have based on a different reference genome (5.57).

What would be the most efficient way to convert the coordinates based on one reference to the latter reference genome?

[GenoMax]

What kind of comparison are you looking to do e.g. if they are in the same gene/location? You may want to use crossmap (LINK) to lift one of the results over and then do the comparison w.r.t the same genome. Additional tools here.

[shpak.max]

Basically, if something is at site 100000 on Chromosome 2L based on the author's reference genome, I want to know the equivalent coordinate using my reference genome.