Hi..Can anyone suggest a simple way of achieving this. I have several files which ends with extension .vcf . I will give example with two files
In the below files, we are interested in

File 1:

File2:

Index file :

The index file is created based on unique positions from file 1 and file 2. I have that ready as index file. Now i need to read all files and parse data according to the positions here and write in columns.
From above files, we are interested in 4th (Ref) and 6th (Alt) columns.
Another challenge is to name the headers accordingly. So the output should be something like this.


---------- Post updated at 12:48 PM ---------- Previous update was at 10:43 AM ----------

---------- Post updated at 01:45 PM ---------- Previous update was at 12:48 PM ----------

Any help !!

---------- Post updated at 02:21 PM ---------- Previous update was at 01:45 PM ----------

Code:

open INDEX,"49_unique_positions.txt" or die $!;
open WRITE,">hap.txt" or die $!;
@index = <INDEX>;
#print "$index[0]";
#while (<INDEX>)
#{

#}
@files = @ARGV;
foreach (@files){
print "file: $_ \t $index[0]\n";
$file = $_;
open F,$file or die $!;
while ($line=<F>){
chomp ($line);
@array = split(/\t/,$line);
print "$array[1] \n";
}
}

From above code which i have wrote so far, i am able to read index file in to array and reading file by file according to wild character given on argument, i read the input file one by one, and printing the positions in to array. Can anyone suggest how i can proceed further by comparing index positions with the current positions which are in array and print out wanted result.