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SVDetect linking -conf svdetect.conf SVDetect filtering -conf svdetect.conf SVDetect links2SV -conf svdetect.conf |
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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.
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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Optional: Install SVDetectWe 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 Install SVDetect scriptsNavigate to the SVDetect project page More information: Download the code onto TACC.
Move the Perl scripts and make them executable
Install required Perl modulesSVdetect 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:
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Return to GVA2019 GVA2020 course page.