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Changing output directory for bamtools split

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.

bamtools sge
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written by phosphorus • phosphorus

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

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written by cpad0112 cpad0112

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

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written by phosphorus • phosphorus

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

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written by GenoMax GenoMax

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"

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written by phosphorus • phosphorus

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