To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

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

rbrnsrbrns DFCIMember
edited September 2016 in Ask the GATK team

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!

Issue · Github
by Sheila

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

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @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

  • rbrnsrbrns 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 · Github
    by Sheila

    Issue Number
    1360
    State
    open
    Last Updated
    Assignee
    Array
    Milestone
    Array
  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @rbrns
    Hi,

    The current MarkDuplicates does not use UMIs at all. The UMI work is in progress.

    -Sheila

Sign In or Register to comment.