Duplicates in Whole Exome Sequence Data

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?

whole exome sequence data

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updated 10.2 years ago by DG

• written 10.2 years ago by haiying.kong

1 answer

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

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written 10.2 years ago by DG

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