Due to tabix constraints, I need to sort a vcf so that contigs and then positions within contigs occur in numerical order in the vcf. I don't know if the following will sort positions within contigs, but I tried this:
cat in.vcf | vcf-sort -c > out.vcf
but was informed:
Old version of sort command installed, please run without the -c option.
I've read that can cause problems here. Further, my contigs are't numeric, but are something like this: 'Erumb1_s00000030'.
I see two possible solutions. (1) I am on Mac OS Mojave, and if there were a way to install the a new unix-style sort, I could use it. I tried homebrew and didn't find anything. (2) there are likely some bash commands that would do it. If anyone has an idea in either of these directions, I would appreciate it.