- The first sort can be omitted if the file is already name ordered
samtools sort -n -o namesort.bam example.bam
必须是-n，不能省略
- Add ms and MC tags for markdup to use later
samtools fixmate -m namesort.bam fixmate.bam
-m不能少
- Markdup needs position order
samtools sort -o positionsort.bam fixmate.bam
- Finally mark duplicates
samtools markdup positionsort.bam markdup.bam