<p>Why do we remove duplicates from BAM files while using Samtools?
When we have paired end data we can remove duplicates as a fragment OR as a pair. How do each of these methods differ?</p>

<p>I would personally recommend using Picard for marking or removing duplicates. If you have a paired data, then both reads for a pair will be used to select duplicates. In this case, if there is another pair that has both of its reads aligning at the same exact location as this pair, then one of these would be marked as duplicates. For fragment reads, location of only one read will be used to mark the duplicates.</p>
