SAMtools tview mapped reads viewer

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