Exercise 1.2: Visualising BAM files

• Click into the terminal in RStudio
• Type samtools tview data/Sample.bam, and click <Enter>.
• Follow the tips below to move around the alignment with your cursor.
• Task 1: Can you identify Variants, i.e. systematic differences from the Reference?
• Task 2: Also try samtools tview data/Sample.bam --reference data/hg19_MT.fasta

Tip

• Use your cursors to move left and right
• Use space or Ctrl-L to make bigger jumps to the right
• Use or Ctrl-H for bigger jumps to the left.
• Type ? to get a quick help
• Type q to quit.