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

• -o : output file name
• –reference : input reference that the reads were mapped against
• last thing: is the name of the bam file

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

• makes sorted.bam.bai file
• We don’t need to open this, it just has to be in the same folder

3/ View

samtools tview sorted.bam test_targets.fasta

• shows the ref seq along the top
• then the reads. has a letter where it differs from the ref.
• move along alignment: space bar; delete
• press ? for more info about moving around