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Breakdancer + Squaredancer

Hi all,

I am trying to find the best workflow to discover structural variants using whole genome paired-end data. The data may consist of normal-tumor pairs.

A web page for TIGRA_SV ( http://tvap.genome.wustl.edu/tools/tigra-sv/ ) introduces a workflow combining BreakDancer and SquareDancer. However, a download button in the SquareDancer page ( http://tvap.genome.wustl.edu/tools/squaredancer/ ) does not seem to work now.

Please let me know if any of you have information about availability of SquareDancer or alternative workflows (using PINDEL instead of SquareDancer??).

Best wishes,

Hiro.

sv software
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updated by Chris Miller Chris Miller • written by Hiroyuki Mishima • Hiroyuki Mishima

1 answer

The squaredancer code is buried in one of the other repos. Here's a direct link to the perl script: https://github.com/genome/gms-core/blob/master/lib/perl/Genome/Model/Tools/Sv/SquareDancer.pl

• 171 views • link
written by Chris Miller Chris Miller

Thank you so much. I will check the SquareDancer code and related scripts on GitHub.

• 0 views • link
written by Hiroyuki Mishima • Hiroyuki Mishima

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