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# How does Picard's MarkDuplicates handle unique molecular barcodes and PCR error?

DFCIMember
edited September 2016

Hello,

I'm interested in using unique molecular barcodes to help distinguish what is PCR error in my samples. My current understanding of how MarkDuplicates chooses a "best-pair" is that it chooses this best pair based on a high sum of base quality scores. Sequences containing PCR errors can also have great base qualities. Has any additional logic been implemented to help distinguish reads containing PCR errors from the original template sequence when using unique molecular barcodes?

Thank you!

Tagged:

#### Issue · Github October 2016 by Sheila

Issue Number
1321
State
closed
Last Updated
Assignee
Array
Milestone
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Closed By
chandrans

@rbrns
Hi,

Sorry for the late response. It is true the tool currently uses the start position of the reads and chooses the"best read" that has the highest base and mapping qualities.

However, there is a tool in Picard that is in active development.
Right now it is an alpha tool, but it can deduplicate reads based on UMI.

-Sheila

• DFCIMember

Thank you for getting back to me!

Can you clarify your first statement:

"It is true the tool currently uses the start position of the reads and chooses the"best read" that has the highest base and mapping qualities."

Does this mean that within a set of reads with one UMI that the program still chooses the 'best read' based on base and mapping quality for this one UMI? Or does markduplicates completely disregard the UMI at this point?

Thank you again!

Issue Number
1360
State
open
Last Updated
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Array
Milestone
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