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Old 06-28-2010, 10:09 AM   #1
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Location: Philadelphia

Join Date: May 2010
Posts: 3
Default bwa missing quality


I have encountered a problem while using bwa aligner.
After using bwa version 0.5.8a on fastq files I checked the sam file for the reads with missing quality e.g. "*",
and got quite many 100 . Fastq files have quality information on those reads.

Here is one of examples of the read in fastq and in sam format:



SOLEXA-DELL_0060:6:44:18581:16891#0 99 chr1 159308947 60 76M = 159309107 236 CAAGCAGTCAGTGGGATGGGGAGCATCTTCCGCAAGAAATGGGGGTGTTTAAGGAGGCCCCCAAGATGAGCTAAAA * XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 RG:Z:OP2.2L06

My question is why the value for the quality is missing in sam file?

I've already asked this question on the mailing list (
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bwa missing quality

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