As Nathan showed you yesterday, the main type of output from aligning reads to a databases is a binary alignment file, or BAM file. These files are compressed, so they can't be viewed using standard unix file viewers such as more, less and head. Samtools allows you to manipulate the bam files - they can be converted into a non-binary format (SAM format specification here) and can also be ordered and sorted based on the quality of the alignment. This is a good way to remove low quality reads, or make a bam file restricted to a single chromosome.
We'll be focusing on just a few of samtools functions in this series or exercises:
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samtools view -bH -o outfile_view.bam infile.bam
samtools sort
samtools count
samtools index aln.sorted.bam |
Exercise 1: counting mapped vs unmapped reads in a bam file
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