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Old 11-19-2010, 07:28 AM   #1
maricu
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Default 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
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Old 11-19-2010, 08:25 AM   #2
nilshomer
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BWA does not consider quality scores so you need to convert the quality scores in the SAM/BAM file to sanger before variant calling.
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Old 11-19-2010, 08:38 AM   #3
m_elena_bioinfo
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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
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Old 11-19-2010, 12:18 PM   #4
bioinfosm
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Quote:
Originally Posted by nilshomer View Post
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!
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