If the file referred to by $ARGV should be appended to instead of overwritten then use the following code. Since you aren't actually using INP, I've removed it.
$file = "$ARGV";
open OUT, ">> $file"
or die "Cannot open file: $!";
@out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV
print OUT @out;
A better way to write that is shown below. The top three lines assume that this is a standalone script which it may not be.
my $file = $ARGV;
open my $out, '>>', $file;
my @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[
print $out @out;
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