Calling structural variants from capture data

Heisman · 08-08-2011, 08:03 AM

Hey,

I tried searching a bit but I'm sadly so ignorant with respect to this question that I'm not able to find things easily. If I wanted to call structural variants from whole exome or custom targeted data, what would be the best algorithms/software to use? Names of software or links to papers would suffice. Thanks!

Heisman · 04-02-2012, 04:39 PM

Any input on this? Does anybody do this sort of thing and if so, do you have any advice? I know a lot of people want read depth/paired read/split read support of SV calls, but which algorithms would be "best" for capture data? Thanks!

msalm · 04-16-2012, 04:38 AM

Hi there,

some options are:

ExomeCNV
http://bioinformatics.oxfordjournals...7/19/2648.full

VarScan2
http://genome.cshlp.org/content/earl....full.pdf+html

Control-FREEC
http://www.ncbi.nlm.nih.gov/pubmed/22155870

ExomeCopy
http://www.degruyter.com/view/j/sagm...xml?format=INT

CONTRA
http://www.ncbi.nlm.nih.gov/pubmed/22474122

cn.mops
http://nar.oxfordjournals.org/conten...abstract?ct=ct

Hope this helps!

Heisman · 04-16-2012, 08:01 AM

Thank you, I will look into some of these. I decided to go on a literature binge over the last week or two and try to see what's out there... there isn't much for structural variation that is specific to capture. It'll be interesting to see what type of pipeline I put together.

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08-08-2011, 08:03 AM	#1
Heisman Senior Member Location: St. Louis Join Date: Dec 2010 Posts: 535	Calling structural variants from capture data Hey, I tried searching a bit but I'm sadly so ignorant with respect to this question that I'm not able to find things easily. If I wanted to call structural variants from whole exome or custom targeted data, what would be the best algorithms/software to use? Names of software or links to papers would suffice. Thanks!

04-02-2012, 04:39 PM	#2
Heisman Senior Member Location: St. Louis Join Date: Dec 2010 Posts: 535	Any input on this? Does anybody do this sort of thing and if so, do you have any advice? I know a lot of people want read depth/paired read/split read support of SV calls, but which algorithms would be "best" for capture data? Thanks!

04-16-2012, 04:38 AM	#3
msalm Junior Member Location: London Join Date: Apr 2012 Posts: 3	Hi there, some options are: ExomeCNV http://bioinformatics.oxfordjournals...7/19/2648.full VarScan2 http://genome.cshlp.org/content/earl....full.pdf+html Control-FREEC http://www.ncbi.nlm.nih.gov/pubmed/22155870 ExomeCopy http://www.degruyter.com/view/j/sagm...xml?format=INT CONTRA http://www.ncbi.nlm.nih.gov/pubmed/22474122 cn.mops http://nar.oxfordjournals.org/conten...abstract?ct=ct Hope this helps!

04-16-2012, 08:01 AM	#4
Heisman Senior Member Location: St. Louis Join Date: Dec 2010 Posts: 535	Thank you, I will look into some of these. I decided to go on a literature binge over the last week or two and try to see what's out there... there isn't much for structural variation that is specific to capture. It'll be interesting to see what type of pipeline I put together.