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    I don't know which file your "chromosome order" numbers correspond to, but you need the -n numeric flag to sort them numerically versus lexically. Commented Mar 12, 2020 at 17:54
  • Thank you for you response, I have one file ``` file.avinput ``` with the chromosomes - I'll edit my question to give more detail of this. Each line is a variant with columns of chromosome number followed by position of the variant at that chromosome. I have since tried a few with -n but having the same trouble Commented Mar 12, 2020 at 18:04
  • It's good to anonymize your data, but be sure to represent the structure, too -- commas, tabs, columns, etc. Commented Mar 12, 2020 at 18:07
  • @DN1 Post a few lines of the files you want sorted. It makes it much easier to understand your problem - especially for non-bioinformaticians. Commented Mar 12, 2020 at 18:07
  • Thank you for these comments, I've had a go. Unfortunately I only have a biology background with little linux experience so not sure if I have copied this over with full clarity, but hopefully it's more clear now. I believe the file should be tab separated Commented Mar 12, 2020 at 18:16