samtools view -X <bam file>
    Convert bitwise FLAG to human readable FLAG.
    
samtools flagstat <bam file>
    Print number of mapped reads and so on.
    
samtools view -H <bam file>
    check if the bam files is sorted. 
    http://biostar.stackexchange.com/questions/5273/is-my-bam-file-sorted  

Manual Reference Pages - samtools

how to extract unique hits from bam files

samtools view -q 1 <bam file>

        You can use samtools view -q 1 to only output uniquely mapped reads
        (and omit both unmapped and ambiguous ones). Ambiguous reads that can
        be mapped to different locations with the same score have mapping
        quality 0 in BWA.
        
samtools view bwa.bam | grep "XT:A:U" 

        BWA outputs have XT tag set to "U". 

http://seqanswers.com/forums/showthread.php?t=8334