I just came across this on Biostar: http://www.biostars.org/p/64687/
Question: How to sort bed format file
2
Is there any tools or commands to sort bed format file? The correct order is chr1, chr2, chr3, chr4,..., chr22, chrX, chrY.
3
GNU sort can now sort in alpha-numeric order. See option "-V, --version-sort" of the following version "sort (GNU coreutils) 8.17".
Here is an example:
$ echo -e "chr10\t1\t2\tA\nchr2\t1\t2\tB\nchr1\t1\t2\tC"
chr10 1 2 A
chr2 1 2 B
chr1 1 2 C
And the result is:
$ echo -e "chr10\t1\t2\tA\nchr2\t1\t2\tB\nchr1\t1\t2\tC" | sort -k1,1V
chr1 1 2 C
chr2 1 2 B
chr10 1 2 A