Question

Breakdancer + Squaredancer

0

Entering edit mode

10.6 years ago

Hiroyuki Mishima • 0

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 • 2.7k views

ADD COMMENT • link updated 10.6 years ago by Chris Miller 22k • written 10.6 years ago by Hiroyuki Mishima • 0

score 1 · Answer 1 · 2013-10-01

1

Entering edit mode

10.6 years ago

Chris Miller 22k

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

ADD COMMENT • link 10.6 years ago by Chris Miller 22k

0

Entering edit mode

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

ADD REPLY • link 10.5 years ago by Hiroyuki Mishima • 0