Changing output directory for bamtools split

Question

[phosphorus]

Hello,

I am using bamtools to split a bam file on SGE (Sun Grid Engine). However, all the split files are located in the same directory as my script. Is it possible to edit my script so that I can specify the directory where the split files should be put?

There seems to be an 'output redirection' option on SGE but from the documentation it only seems to apply to the standard output/error SGE files, rather than the files generated from bamtools. I am wondering if there is any command that can redirect the latter to a specific directory.

[cpad0112]

did you try supplying the output directory path (directory path+ file path) in -out option?

[phosphorus]

When I tried using the -out option I got an error message...

ERROR: Some problems were encountered when parsing the command line options: An unrecognized argument was found: -out

[GenoMax]

Are you using the latest version of bamtools? Post entire command line.

[phosphorus]

I am using bamtools version 2.5.1. I typed the following command: bamtools split -in test.bam -reference -out test_splitbamdir

The error log shows the following:

ERROR: Some problems were encountered when parsing the command line options: An unrecognized argument was found: -out An unrecognized argument was found: ../test_splitbamdir/

For a complete list of command line options, type "path_to_bamtools/bamtools help split"