SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
CNV analysis using sequencing data? foxyg General 13 12-21-2011 05:37 AM
retain multihit reads for CNV analysis jorge Bioinformatics 0 08-30-2011 12:41 AM
Which technology is better for CNV detection, SOLiD or Solexa? El Mariachi SOLiD 0 12-30-2010 12:45 AM
Target enrichment and CNV analysis gendxdoc Sample Prep / Library Generation 1 09-27-2010 04:47 AM
using BWA to align SOLiD fastq files from 1000 Genomes tgenahmet Bioinformatics 1 10-15-2009 05:19 PM

Reply
 
Thread Tools
Old 05-13-2011, 09:19 AM   #1
rcorbett
Member
 
Location: canada

Join Date: Sep 2009
Posts: 29
Default CNV analysis on Illumina / Solid genomes

Hi all,

I had a look at the wiki and I see there are many tools available for getting copy number changes from read alignments. I am wondering if there is a particular accepted tool that comes most highly recommended.

I am most often comparing 30X tumour to 30X normal, and I know from experience that GC bias correction is necessary.

Freec seems like a good candidate however, when comparing matched tumour normal pairs the applied bias correction seems a little less vigorous than I would like.

Any information is appreciated!
rcorbett is offline   Reply With Quote
Old 07-05-2012, 04:36 AM   #2
valeu
Member
 
Location: Paris

Join Date: Sep 2008
Posts: 69
Default

I think when you have 30X coverage, FREEC must be a good choice. In addition to copy numbers it will detect LOH regions and it could tell you which regions of gain/loss/LOH are likely to be somatic/germline.
valeu is offline   Reply With Quote
Old 07-05-2012, 11:04 AM   #3
unagaswamy
Member
 
Location: Texas

Join Date: May 2010
Posts: 13
Default XHMM for CNV analysis

Hi,

Has anyone tried the xhmm CNV tool on exomes?

http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml

I tried it on five exome bams and I always get an empty vcf file!

Thanks,
-Uma
unagaswamy is offline   Reply With Quote
Old 07-06-2012, 07:27 AM   #4
CraigJ
Junior Member
 
Location: Indiana University, Indiana, USA

Join Date: Jul 2012
Posts: 8
Default

I haven't used this software myself, but I have been looking into CNV software as well, and saw this. While it isn't what I'm looking for, it seems like it could be very useful to you since you are using tumor/normal comparison data.

The software is VarScan (http://varscan.sourceforge.net/), and a specific section of the software is for finding CNV between normal/abnormal(tumor) samples. Here is the section on that: http://varscan.sourceforge.net/copy-number-calling.html

Cheers.
CraigJ is offline   Reply With Quote
Reply

Tags
cnv, copy number, read alignment

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 12:55 AM.


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