一、samtools markdup的使用

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

二、sambamba markdup的使用

一行命令即可：

sambamba markdup --overflow-list-size 600000 --tmpdir='./' -r raw.bam rmdup.bam

补充：
sambamba的安装方法如下：
比对结果去重软件：sambamba的安装以及安装出错解决办法 - 简书 (jianshu.com)

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