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

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

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

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!