This was a doozy to track down, but I have been having issues with bed sorting for plant species with chloroplasts when building track hubs. Similar to issues here.
e.g. here's the end of a sorted.chrom.sizes that cause issues because it is sorted differently depending on if you do case-sorting or not:
The solution is to case sort before running bedtools complement. Then sort the non callable sites file using bedSort (for whatever reason relating to locale, sort doesn't work for this). This seems most robust to variation on different linux configurations of locale.
This was a doozy to track down, but I have been having issues with bed sorting for plant species with chloroplasts when building track hubs. Similar to issues here.
e.g. here's the end of a sorted.chrom.sizes that cause issues because it is sorted differently depending on if you do case-sorting or not:
The solution is to case sort before running bedtools complement. Then sort the non callable sites file using bedSort (for whatever reason relating to locale, sort doesn't work for this). This seems most robust to variation on different linux configurations of locale.