I'm trying to control which reads are mapped to a reference genome by adjusting the the -T parameter in bwa mem, which is the minimum acceptable alignment score. The only problem is that reads with an alignment score below the threshold are being mapped anyway. I can see this when using samtools view to visualize the bam file, reads with an AS value less than the threshold are there. My data is paired end, so I tried doubling the threshold to account for both reads, but that didn't work either.
What's going on here? Do some settings in bwa mem interfere with -T?