I'd like to report and share some information which is not described in README or manual but user should know.
1) The bam files (for normal and tumor) must be indexed.
2) Beware if you give some parameters which are symbolic links.
The run_novoBreak.sh scripts parses the parameters using 'readlink' function, that automatically converts a symbolc link to its original path. It might cause a problem.
In my case, as an example, I made a symbolic link to the reference genome and built bwa index with the symbolic link by some reasons. But due to the readlink function, the path is converted to its original path and my experiment was stopped with an error that bwa could not find the index (tens of hours after beginning!!).
These are not critical issues, but I spent many hours to find out the reasons and re-run my experiment.
Thanks,
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Hi,
I'd like to report and share some information which is not described in README or manual but user should know.
1) The bam files (for normal and tumor) must be indexed.
2) Beware if you give some parameters which are symbolic links.
The run_novoBreak.sh scripts parses the parameters using 'readlink' function, that automatically converts a symbolc link to its original path. It might cause a problem.
In my case, as an example, I made a symbolic link to the reference genome and built bwa index with the symbolic link by some reasons. But due to the readlink function, the path is converted to its original path and my experiment was stopped with an error that bwa could not find the index (tens of hours after beginning!!).
These are not critical issues, but I spent many hours to find out the reasons and re-run my experiment.
Thanks,