maintain_header_sort.sh

## imagine we have a file with one line header, and we want to keep the header after sorting
## use subshells http://bash.cyberciti.biz/guide/What_is_a_Subshell%3F  
(sed -n '1p' your_file; cat your_file | sed '1d' | sort) > sort_header.txt

## if you have two header lines and want to keep both of them:
(sed -n '1,2p' your_file; cat your_file | sed '1,2d' | sort) > sort_header.txt

## if you have many lines starting with "#" as header, like vcf files
(grep "^#" my_vcf; grep -v "^#" my_vcf | sort -k1,1V -k2,2n) > sorted.vcf

## one can also use awk
cat my_vcf | awk '$0~"^#" { print $0; next } { print $0 | "LC_ALL=C sort -k1,1V -k2,2n" }'

## I am a useless cat user :) http://stackoverflow.com/questions/11710552/useless-use-of-cat