Correct operation sequence samtools`markdup`

Specific examples of 5 one-step process to find the mutation
samtools markdupproper sequence of operations

1. The first sort can be omitted if the file is already name ordered

samtools sort -n -o namesort.bam example.bam

Must -nnot be omitted

2. Add ms and MC tags for markdup to use later

samtools fixmate -m namesort.bam fixmate.bam

-mcan not be less

3. Markdup needs position order

samtools sort -o positionsort.bam fixmate.bam

4. Finally mark duplicates

samtools markdup positionsort.bam markdup.bam