Samtools can be used to select reads above certain mapping quality.
samtools view -h -b -q 30 aligned.bam -o above.mapQ30.bam
But, how to select a read below certain mapping quality - all aligned reads below mapQ 30?
I know it can be done using awk. But, the pipeline gets lengthy and time consuming when first need to convert bam to sam - separate header - use awk for mapQ below 30 - add header - sam file - convert to bam. Really, its taking a lots of time.