If the file referred to by $ARGV[1] 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[1]";

open OUT, ">> $file"
        or die "Cannot open file: $!";

@out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] 
+2>&1`;

print OUT @out;

close OUT;
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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.

#!/usr/bin/perl
use strict;
use warnings;

use autodie;

my $file = $ARGV[1];

open my $out, '>>', $file;

my @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[
+0] 2>&1`;

print $out @out;

close $out;
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