Log into your instance, create a new directory, navigate to that directory:
cd /mnt
mkdir sam
cd sam
# Get the makefile.
wget https://raw.githubusercontent.com/ngs-docs/angus/2014/files/Makefile-samtools -O Makefile
A series of exercises will show what the SAM format is and how it changes when the query sequence is altered and how that reflects in the output.
Also, for the speed of result generation here is a one liner to generate a bamfile:
# One line bamfile generation. bwa mem index/sc.fa query.fa | samtools view -bS - | samtools sort - results
This will produce the results.bam output.