BOL

To do sam to bam conversion, follow the following commands :- 

$ samtools view -b -S file.sam > file.bam

Then you will need to use 

$ samtools sort file.bam file-sorted

followed by

$ samtools index  file-sorted.bam

in order to get an indexed file.

If you just type 

$ samtools

or samtools followed by the name of one of the samtools commands, you will get a few lines of help giving the correct syntax for that command,