samtools view -bS test.sam > test.bam
samtools sort test.bam -o test_sorted
samtools index -b test_sorted.bam
samtools tview test_sorted.bam ref.fa
samtools view -bS test.sam > test.bam
samtools sort test.bam -o test_sorted
samtools index -b test_sorted.bam
samtools tview test_sorted.bam ref.fa