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