SAMtools recipes

Remove duplicates

If you BAM file has no duplicated marked, you may use samtools to mark and remove then as follows.

First, sort the BAM file on query name::

samtools sort -@ 4 -n data.bam data.sorted.byquery.bam

You may need to fix the mate::

samtools fixmate -m -r data.sorted.byquery.bam fixmate.bam

Sort back to coordinate::

samtools sort -@ 4 fixmate.bam -o fixmate.sorted.bycoord.bam

Finally, remove the duplicates (with markdup)::

samtools markdup -s -r --fixmate.sorted.bycoord.bam data.markdup.bam