I don’t understand this part of the code:

my $col = "";  
foreach my $key (keys %sampleValue){
    my @col1 = split("\t",$sampleValue{$key});
    $col = $col1[1].",".$col;
}
chop($col);
print $col,"\n"; ## string of all the columns I am interested in
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So far as I can see, %sampleValue contains entries of the form Header1 => 1, Header2 => 2, Header5 => 5, ..., so splitting each value on tabs does nothing? In any case, you need to produce an array here, not a string:

my @cols = sort values %sampleValue;
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Then you can use an array slice:

## Reading the sample Value file
while (<$IN>)
{
    chomp;
    print $_, "\n";
    my @line = split "\t";
    @line = @line[@cols];   # <-- Use array slice here
    ...
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Some notes:

• Always use strict; and use warnings;.
• It would help if you provided sample data and expected output along with the code.
• Update: Just checking: you do realise that in Perl (as in C), array indices start at 0, not 1?

Hope that helps,