SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
failed to install pysam shown below andy123 Bioinformatics 3 03-27-2011 03:29 AM
Sam flags for bwa-aligned paired end reads with identical + / - strand coordinates spark Bioinformatics 0 03-09-2011 05:00 AM
BWA search strand guillaum Bioinformatics 0 04-21-2010 09:04 AM
In Sequence: UCLA Team Maps Methylation in Arabidopsis At Single-Base Res; Larger Gen Newsbot! Illumina/Solexa 0 03-18-2008 03:45 PM
In Sequence: Illumina GA’s Deep Coverage Shown to Be Useful for Profiling, Discovery Newsbot! Illumina/Solexa 0 02-26-2008 03:20 PM

Reply
 
Thread Tools
Old 10-13-2010, 03:33 PM   #1
Calle
Junior Member
 
Location: Sweden

Join Date: Feb 2009
Posts: 5
Default BWA --> SAM: sequence shown of strand where it maps

Hi,

I mapped some Illumina 75x2 reads using bwa (Version: 0.5.8). When I used samtools pileup I noticed that I have loads os variant calls everywhere. Upon further investigation I noticed that the nt-sequence in the sam file is presented on the strans where the read maps and not on the forward strand of the reference (as it should be?).

I have not had this problem with pileups using any other aligner. Is this common behavior for bwa? If so, does anyone know what can be done?
Am I missing something here?

Thanks

Last edited by Calle; 10-13-2010 at 03:48 PM.
Calle 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 07:37 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO