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Code Block
titleCommands to run SNVDetect
SVDetect linking -conf svdetect.conf
SVDetect filtering -conf svdetect.conf
SVDetect links2SV -conf svdetect.conf
Warning
titlePossible errors on idev nodes

In reviewing these tutorials these commands were not executing for me in idev sessions for unknown reasons. By chance I had an idev session time out with me noticing and I noticed it did run on the head node. Try the above commands 1 at a time, but if you see error messages like the following logout of your idev session with the logout command, and then execute them 1 at a time on the head node. While this is not the best citizenship, the program gave no indications of being a problem.

No Format
Config/General.pm did not return a true value at /corral-repl/utexas/BioITeam/bin/SVDetect line 48.
BEGIN failed--compilation aborted at /corral-repl/utexas/BioITeam/bin/SVDetect line 48.

Feedback in zoom on if the commands either work on an idev session for you, or if they do not would be appreciated.


Take a look at the resulting file: 61FTVAAXX.ab.sam.links.filtered.sv.txt. Another downside of command line applications is that while you can print files to the screen, the formatting is not always the nicest. On the plus side in 95% of cases, you can directly copy the output from the terminal window to excel and make better sense of what the columns actually are

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Expand
titleclick here for installation instructions

Optional: Install SVDetect

We have installed SVdetect for you already as installation is a bit difficult (though still much easier than the alternatives listed in the introduction). You can verify it's location using which SVDetect in your $PATH under $BI/bin. One of the advantages (or disadvantages) of using the communal resource is that someone else can update all the necessary programs and packages for you. Alternatively, you can make a personal copy of the program yourself using the following commands. NOTE that this is presented mostly to underscore how spoiled we are with modules and the BioITeam.

Install SVDetect scripts

Navigate to the SVDetect project page

More information:

Download the code onto TACC.

Code Block
wget http://downloads.sourceforge.net/project/svdetect/SVDetect/0.80/SVDetect_r0.8b.tar.gz
tar -xvzf SVDetect_r*.tar.gz
cd SVDetect_r*

Move the Perl scripts and make them executable

Code Block
cp bin/SVDetect $HOME/local/bin
chmod 775 scripts/BAM_preprocessingPairs.pl
cp scripts/BAM_preprocessingPairs.pl $HOME/local/bin

Install required Perl modules

SVdetect requires a few Perl modules to be installed. In the default TACC environment, you can use the cpan shell to install most well-behaved Perl modules (with the exception of some complicated ones that require other libraries to be installed or things to compile). Here's how:

Code Block
titleInstall Perl modules required for SVDetect
This can not be done from an idev session
login1$ cpan
# choose yes to do as much automatically as possible and 'local::lib' for how you want to install modules as you don't have admin rights on TACC
...
cpan[4]> install Config::General
...
cpan[4]> install Tie::IxHash
...
cpan[4]> install Parallel::ForkManager
...
cpan[4]> quit
login1$

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