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Old 03-26-2010, 10:24 AM   #4
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
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Originally Posted by dnusol View Post
Hi nilshomer, sorry for getting back to this thread, but do you know if Picard is able to remove duplicates from single-reads? Samtools manual does not recommend it but I am not sure if it is a matter of implementation or a real technical issue on the single read part which I don't get.

If you have high coverage (say 50x for 50bp reads), then it becomes very likely that multiple single end reads will start at the same coordinate. You will then wont be able to tell coverage from PCR duplicates. For PE or LMP reads, both ends can be used to determine duplication, since the insert size has its own distribution.
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