SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA parameters affects SNP calling with samtools? hellohenry Bioinformatics 5 08-21-2012 07:35 PM
parameter set of bwa-samtools for snp calling heiya De novo discovery 10 04-25-2012 07:27 PM
Samtools SNP calling vidhya Bioinformatics 3 04-07-2011 07:17 AM
MAQ vs BWA/SAMTools - differences in SNP calling algorithm? mard Bioinformatics 2 10-20-2010 03:17 PM
SAMtools and SNP calling Jan Bioinformatics 2 09-16-2010 02:01 PM

Reply
 
Thread Tools
Old 08-21-2012, 07:05 PM   #1
heiya
Member
 
Location: China

Join Date: Nov 2011
Posts: 14
Default snp calling with bwa-samtools

hi,everyone! I do wet experiment verification for my heterozygous snp found by bwa-samtools in rice genome recently,however only three of fourteen got experiment support, the rest didn't get! I have checked the reads coverage in the position of SNPs, all the indication are that they are SNPs!
Could someone explain that?

all the reply are appreciated!
heiya is offline   Reply With Quote
Old 08-21-2012, 07:20 PM   #2
adaptivegenome
Super Moderator
 
Location: US

Join Date: Nov 2009
Posts: 437
Default

1. Sequencing error
2. Mapping error
3. Validation error.

Those are 3 possibilities, I'm sure there are more. You don't provide much info so it's hard to know for sure.
adaptivegenome is offline   Reply With Quote
Old 08-21-2012, 07:27 PM   #3
wzhjlau2009
Junior Member
 
Location: china

Join Date: Jun 2011
Posts: 5
Default

i also meet the problem,can we have a chat? my email:wzhjlau@163.com QQ:872664567
wzhjlau2009 is offline   Reply With Quote
Old 08-21-2012, 10:51 PM   #4
oyvindbusk
Member
 
Location: Norway

Join Date: Jan 2011
Posts: 14
Default

Hello heiya, my experience is that using samtools with default settings will give you a high number of false positives, this could be what you are seing.

You could try running snp-calling with the GATK using the built-in recalibration options. GATK has quite a low number of false positives. Compare the results from GATK with your existing results, and see what you get.

oyvindbusk 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 01:12 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO