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

##</code><code>##

my @cols = sort values %sampleValue;

##</code><code>##

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