perl `system()` does what it wants (just like april in a dutch saying)

[mmterpstra]

According to perldoc you should catch all of your system calls with a check of $? if you want your programs to exit nicely if the shell gives an error. Example below.

#set -x or && could be used. Here both are used. 
my $indexcmd = "set -x && bgzip -c $invcf > $outvcf && tabix -p vcf $outvcf";
        my $ret = `$indexcmd`;
        $? == 0 or die "system cmd `$indexcmd` failed: $ret\n exit code: $?";

Example of affected scripts (not exhaustive ):

• createBWAandSAMtoolsIndices.pl
• per_folder/index_creator.pl
• createLocalRealignmentIntervals.pl
• runpindel.pl
• maybe every perl script that contains system().