SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
samtools pileup BioSlayer Bioinformatics 9 01-16-2012 04:10 AM
samtools pileup raghu1990 Bioinformatics 0 06-28-2011 03:26 AM
samtools pileup wisosonic Bioinformatics 0 05-11-2011 05:57 AM
Tophat v1.1.4 bug - cannot handle non-numeric versions of Samtools adumitri Bioinformatics 4 01-10-2011 06:18 AM
samtools pileup format foxyg Bioinformatics 3 11-16-2010 08:25 AM

Reply
 
Thread Tools
Old 02-11-2011, 07:36 AM   #1
dg.pooja
Junior Member
 
Location: India

Join Date: Nov 2010
Posts: 2
Default Different versions of samtools-pileup

Hello,

** I have used pileup function with -vcf options both with samtools versions 0.1.7a and 0.1.12a

** I found the pileup output from both versions of samtools to be very different.

** Using the same aligner with exact same options, samtools 0.1.7a is giving me 452 unique SNVs and the version 0.1.12a 251 unique SNVs.

** There are 196 SNVs that are common to both versions of samtools. This is after I use varfilter with default parameters with SNP quality cutoff of 20.

** I understand that the old version of samtools use the MAQ SNP calling criteria and we have not used -A option with samtools version 0.1.12a, hence have not forced MAQ calling criteria.

*** I am confused with the data and would like to understand why there is such difference in results between the two versions of samtools.


Can any one help in this regard ?

Thank you
Pooja
dg.pooja is offline   Reply With Quote
Old 02-11-2011, 08:19 AM   #2
drio
Senior Member
 
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323
Default

The snp caller engine has changed dramatically among those versions. Review carefully the manuals, particularly mpileup.

That being said. The overlapping events sounds a little bit low but it depends on the coverage for your project.
__________________
-drd
drio is offline   Reply With Quote
Old 02-11-2011, 09:39 AM   #3
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 912
Default

Using the -B option on the new pileup command might cause it to behave more like the old pileup.
swbarnes2 is offline   Reply With Quote
Old 02-11-2011, 09:46 AM   #4
drio
Senior Member
 
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323
Default

If I am not mistaken the latest version uses the SOAP model instead of the MAQ model at the core of the snp caller. Let us know if by removing BAQ computations (-B) you get similar results to the old version.
__________________
-drd
drio 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 01:47 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO