I'm running Pindel on small Ion Torrent (single-end reads) bam files. When the insert size specified in the config file is less than detected by the software, Pindel crashes with an error message. Could someone please suggest how to write that error message to a text file?
Here is the command that I use to run Pindel in my Perl script.
my $cmd1 = `$pindel -f $fastafile -i $configfile -c ALL -o $outputfolder`; print $cmd1;