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  • Thank you for this, do you know how I can apply this to a large file, I have 16945 lines with more columns than just the chromosome column - sorry I've only amended my question to detail this now Commented Mar 12, 2020 at 18:19
  • it is still not clear what you need. I showed only approach, if you want to have file lines sorted numerically ascending based on numbers in first column, you only need to cat file1|sort -n > file2. It may help to understand you better, if you provide with 1) input file1 containing 4-5 lines ordered incorrectly; 2) desired properly ordered result file2, you want to get from file1. Commented Mar 12, 2020 at 18:32
  • Sorry about that, I've tried to re-do my example data for more clarity. I've also tried the line you provide in this comment but it gives an empty file Commented Mar 12, 2020 at 18:40
  • When I run just sort -n file1 I see it working, but then I add the > file2 file2 is empty Commented Mar 13, 2020 at 10:21