Is It Necessary To Remove Duplications After Bwa Alignment?

Question

[Tonyzeng]

HI, I got another question here, is it always necessary to find duplicates and remove them after bWA alignment whatever alignment is good or not?

[Pierre Lindenbaum]

see that thread on SE: http://seqanswers.com/forums/showthread.php?t=6854&highlight=large+sample+calls

[Jorge Amigo]

Pierre has been too gentle. I would suggest that you first use the search function here looking for "duplicates" or for "markduplicates", and also to use the "tags" section selecting any of those 2 mentioned tags. you'll find plenty of information there that describes what NGS duplicates are, why we have to consider them specially in the analysis, when it's advisable to remove them and when it's not,...