SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Structural Variants jkozubek Bioinformatics 4 08-22-2016 07:38 AM
Pindel: improved version for indels and structural variants KaiYe Bioinformatics 147 07-17-2016 07:14 PM
Calling structural variants (CNVs) with single-end reads agwe Genomic Resequencing 5 01-18-2016 07:30 AM
SNP calling vs emitting variants Rubal7 Bioinformatics 7 05-13-2013 11:15 AM
Hiseq 2000 paired-end capture data analysis problem-too many variants! lazyworm Bioinformatics 1 08-11-2010 10:03 AM

Reply
 
Thread Tools
Old 08-08-2011, 07:03 AM   #1
Heisman
Senior Member
 
Location: St. Louis

Join Date: Dec 2010
Posts: 535
Default 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!
Heisman is offline   Reply With Quote
Old 04-02-2012, 03:39 PM   #2
Heisman
Senior Member
 
Location: St. Louis

Join Date: Dec 2010
Posts: 535
Default

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!
Heisman is offline   Reply With Quote
Old 04-16-2012, 03:38 AM   #3
msalm
Junior Member
 
Location: London

Join Date: Apr 2012
Posts: 3
Default

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!
msalm is offline   Reply With Quote
Old 04-16-2012, 07:01 AM   #4
Heisman
Senior Member
 
Location: St. Louis

Join Date: Dec 2010
Posts: 535
Default

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.
Heisman is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:36 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO