SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to call SNP using known SNP information nkwuji Bioinformatics 1 07-23-2013 09:16 PM
First Call Missing on SOLiD johnadam33 Bioinformatics 9 09-20-2011 07:44 PM
Ti/Tv ratio for known and novel SNP call sets deviates seqpig100 Bioinformatics 1 06-27-2011 09:32 AM
1000 genome SNP call zhanglu295 Bioinformatics 5 03-30-2011 09:57 AM
SNP mapping quality problem ptong7 Bioinformatics 0 12-23-2009 12:22 PM

Reply
 
Thread Tools
Old 03-10-2011, 12:26 AM   #1
pr0t3us
Member
 
Location: Italy

Join Date: Oct 2008
Posts: 12
Default SOLiD SNP CALL Problem

Dear All,

I'm working with SOLiD data. We have sequenced different strains of E.Coli with shotgun approach and our aim was to find variants (SNPs or INDELs).
I have an average coverage of 150X and I run the spectral correction on the reads to improve their quality.

I tried different softwares (Bioscope SNP calling pipeline, MAQ SNP calling pipeline and PASS). I obtain strange results:
- my bacteria seem to be diploides!!!!
- The three software give total different results. (SNPs in different positions)

Do you have any suggestion on how to approch a SNP calling with SOLiD data?

Best

Alex
pr0t3us is offline   Reply With Quote
Old 03-10-2011, 08:54 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

1) It is possible that you are sequencing more than one strain of E. coli. Yes, I know that it should be a pure strain but if it isn't then it might appear to be diploid.

2) How variable (or similar) are your SNP calls? If there is 90% overlap between the programs then this may be fine.
westerman is offline   Reply With Quote
Old 03-17-2011, 07:56 AM   #3
epigen
Senior Member
 
Location: Germany

Join Date: May 2010
Posts: 101
Default

1) SNP callers are generally designed for diploid organisms, check if there is an explicit option for haploid ones.
2) Different parameters (cutoff for mapping quality, base quality, coverage, proximity, location in reads ...) = different SNPs. But the "obvious" SNPs should be detected by all methods. I guess 70% overlap would be okay.
epigen 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 12:59 PM.


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