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Once you have your reads mapped to your reference (a sam file, converted to a bam file):
1/ we need to pileup all the reads by their location: this is sorting by location
samtools sort -o sorted.bam --reference test_targets.fasta NZ281.bam
2/ then we need to index that sorted.bam file [makes it quicker for other stuff to access it at various places]
samtools index sorted.bam
3/ View
samtools tview sorted.bam test_targets.fasta