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Hello,

Sorry if this is the wrong forum for this question - I just thought someone might have an idea/opinion...

Should I trim/filter exome sequencing reads prior to mapping with BWA and variant calling using GATK? I am currently filtering out reads in which <80% of bases have quality>=Q30 but I lose >20% of my reads this way. Does GATK take quality into account therefore rendering pre-mapping filtering unecessary?

Thanks in advance, Kath