You haven't use while loop to read the file line by line after opening the file. You don't have to use <STDIN> when you have initialized $infile before. You use <STDIN> when you want the input from the user/keyboard. Also, you haven't defined your file handler. It should be :

my $infile = "xxx_capillary_SNPs.txt\n"; 
open IN, $infile or die "open infile failed\n";
while(<IN>){

## do your reverse complement
}
close(IN);
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