mark and remove duplicates

[thiNGS]

Hi everyone! if I mark duplicates in my BAM file using samblaster can I remove them using samtools rmdup?
I was wondering if samtools consider the duplicates flagged by the other tool and just remove them or if it marks again the duplicates itself.

[dpryan]

Samtools rmdup doesn't look at the dup flag that is presumably set by samblaster. Instead, just use

samtools view -bF 0x400 original.bam > dedup.bam