SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: A survey of copy-number variation detection tools based on high-throughput se Newsbot! Literature Watch 0 03-12-2013 02:00 AM

Reply
 
Thread Tools
Old 11-01-2014, 01:12 PM   #1
mrfox
Senior Member
 
Location: USA

Join Date: Aug 2010
Posts: 103
Default Germine copy number variation detection?

Hi all,
I have the normal tissue of about 20 cancer patients with family cancer history. We would like to perform exome sequencing to identify germline mutations, especially germline copy number variations but have not much experience. A couple of questions:

1) What will be a good "reference"/normal BAM file? Randomly selecting reads from BAM files of some normal people sequencing data?
2) Assume we have such a BAM files in 1), can we just use public software tools such as VarScan2 to compare the patient's BAM with the reference BAM?

Any input is greatly appreciated!
mrfox is offline   Reply With Quote
Old 12-08-2014, 02:14 PM   #2
etal
Member
 
Location: California

Join Date: Oct 2013
Posts: 23
Default

Quote:
Originally Posted by mrfox View Post
1) What will be a good "reference"/normal BAM file? Randomly selecting reads from BAM files of some normal people sequencing data?
You can use a program like CoNIFER or cn.MOPS to process the samples as a cohort. These programs each use a statistical method to consider all of the given samples in aggregate to determine the "expected" baseline for copy number inference.

Alternatively, CNVkit works more like your proposal, where a reference copy number profile is initially constructed from a pool of normal BAM files and then reused to infer CNVs in individual samples. CNVkit can also operate without any normal-sample reference at all, but results will be slightly noisier.

Quote:
Originally Posted by mrfox View Post
2) Assume we have such a BAM files in 1), can we just use public software tools such as VarScan2 to compare the patient's BAM with the reference BAM?
Yes, you could. Be careful to check that any recurrent CNVs you find aren't simply the result of having a region of unusually high or low read depth in your reference BAM.

Most program for copy number inference will give you some indication of how the reference should be built and whether you should process one sample at a time or the whole cohort at once.
etal 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 04:04 PM.


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