Panel DNA data Remove Duplicates

[cindylanzao]

Hi,all

We are doing panel data for variants calling and need to make it clear whether we should remove the duplicates with picard, I do not know the capture method, so, let us suppose there would be PCR duplicates Reads. The main consideration would lie on the problem of the probable few amount of data would be left if we use picard MarkDuplicates to deal with the supposed PCR duplicate reads. Any suggestions?

Thanks！