samtools tips

Remove duplicates

first, sort the BAM by query name (-n)

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

and fixmate to add MC tag::

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

sort by coordinate for markdup::

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

and finally remove duplicates::

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

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