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chromosome1 100 100 . G T several other columns
chromosome1 110 110 . A C several other columns
chromosome1 200 200 . C T several other columns
chromosome2 125 125 . C T several other columns

use List::Util qw(shuffle);
use strict;
...
    
}

either randomize file first (for example with unix 'shuf') and read fi
+rst line of randomized file or slurp entire file into array and then 
+randomize

...

continue until a new collection of a specified number of random lines 
+is generated, with no lines containing positions on the same chromoso
+me and within X distance of one another.