SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   BWA mapping fastq files with Illumina quality (http://seqanswers.com/forums/showthread.php?t=7965)

maricu 11-19-2010 07:28 AM

BWA mapping fastq files with Illumina quality
 
Hello,

I am still new in these matters, I was told to map illumina reads to the human genome. I was given the fastq files and proceeded to use BWA, everything ran smoothly 'til today when I realised the reads I had mapped had the Illimina base qualities instead of Sanger's . This raised several questions: Why can BWA map fastq files with the Illumina instead of Sanger? What are the consequences of this?? Unmapped reads?? miscalled variants?? I am pretty concerned since the mapping took around two weeks and I am not sure if I need to start from scratch again and remap the fastqs in sanger format. Please, any help will be highly appreciated!!

Tanks,

Maria

nilshomer 11-19-2010 08:25 AM

BWA does not consider quality scores so you need to convert the quality scores in the SAM/BAM file to sanger before variant calling.

m_elena_bioinfo 11-19-2010 08:38 AM

See this post:
http://seqanswers.com/forums/showthread.php?t=5210

I use the patch (http://sites.google.com/site/davidec...edirects=0&d=1) and the option -I in the alignment to convert quality.
It's run perfectly (thanks to Dawe)

ME

bioinfosm 11-19-2010 12:18 PM

Quote:

Originally Posted by nilshomer (Post 29714)
BWA does not consider quality scores so you need to convert the quality scores in the SAM/BAM file to sanger before variant calling.

thats a shift from MAQ which does use base Q values to do alignments. Wouldn't BWA achieve greater efficiency in using base quality values of mis-matches to weigh them and penalize accordingly!


All times are GMT -8. The time now is 06:47 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.