[Bio-bwa-help] handling of Illumina quality filtered reads

[Gísli M. <Gis...@de...>]

Hello,

I am working with fastq data coming off Illumina machines by way of the casava bcl2fastq conversion. Those fastq files have a field in the read header indicating whether the read was quality filtered or not.

As far as I can tell, bwa mem (version 0.7.10) ignores this field. Am I correct and if so, is that intentional? I was sort of expecting this field to be carried forward into the sam file by setting the platform/vendor quality FLAG (0x0200).

Thanks in advance,

Gisli.