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Old 11-07-2009, 02:44 PM   #1
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Location: Seattle WA

Join Date: Nov 2009
Posts: 5
Default Quality values for aligned reads in .sam file

I am mapping ABI solid reads using bwa, and then converting to a sam file and ultimately to a .pilup file using samtools. I am trying to understand the quality values in the sam file. For the unmapped reads the quality values agree with those in the fastq file, but for the mapped reads, I can see no relationship between the quality values in the .sam file and those in the .fastq file, or the mapping quality. I bring this up because I am trying to write my own snp filter, and don't know whether I can trust the reported quality values. I would appreciate any help on this.

Arnold Kas
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