I want to remove duplicates from my bam file.
I use picard MarkDuplicates to remove the duplicates. (REMOVE_DUPLICATES=true)
After I run picard to "remove all duplicates" ,I found in the bam file reads that still flag MarkDuplicates and I found duplicate clusters that are not removed. I thought Picard remove all reads that are flag as Duplicates?
That's why I use samtools rmdup for paired end mode. It remove more reads than picard. But why ?
I thought when I use picard I remove all duplicates (optical and pcr)