Duplicates in Whole Exome Sequence Data

Question

[haiying.kong]

After alignment with BWA, I used Picard tools to treat duplicates and some other stuff. Our data is whole exome sequence data. Should I remove duplicates with Picard tools, or just mark duplicates so that later software could take care for the duplicates?

Answer 1

[DG]

Just MarkDuplicates with Picard, there is no need to remove them. Downstream tools are designed to handle them appropriately.