samtools`markdup`操作的正确顺序

具体实例在5 一步法找基因变异流程
samtoolsmarkdup操作的正确顺序

1. 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

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

samtools fixmate -m namesort.bam fixmate.bam

-m不能少

3. Markdup needs position order

samtools sort -o positionsort.bam fixmate.bam

4. Finally mark duplicates

samtools markdup positionsort.bam markdup.bam