I want to get uniquely mapped reads from bam files aligned with bwa-mem using the -M option (to make it compatible with picard-tools). If I try to use the following command with samtools to get uniquely mapping reads( or reads with mapping quality greater than 10. I get a very high number of around 90% uniquely mapping. I know I can decrease this number using a more strong threshold of mapping quality of 30 or so but I want to know what would be the ideal way to do so and if the bwa-mem needs to be run with different set of parameters to get more reliable alignments. Following are the bwa and samtools commands that I am using.
bwa mem -t 4 -M ref_genome.fasta fastq fastq > samfile samtools view -c -q10 -f 1 -F 12 -S samfile