Ion Torrent Proton PCR duplicates

[IonTom]

For Amplicon Sequencing it is known that a lot of reads will have the same start position. But this is more due to Amplicon sequencing than the Proton.

But how high should the percentage be for Whole Exome Sequencing using the Proton protocols ? I have been seeing values up to 80% or more (using Picard), which seems a bit much. But it could also be due to using single end reads.

Also how to deal with duplicates in Amplicon data ? I have been thinking about removing optical duplicates only.

[snetmcom]

It sounds like you are talking about Ampliseq Exome, which is supposed to have duplicates. It uses primers to amplify the exome, so you would not remove duplicates.