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Criteria for filtering OxoG artifacts in Mutect2

Hello,

What filter criteria should one apply to filter out OxoG artifacts for M2 calls?

Elsewhere in the forum, it is mentioned that "You can use the FOXOG annotation as an estimate of whether the relative support from the two pair orientations indicates bias or not." If this the annotation is to be used for filtering, what is the threshold that to filter out calls that show a bias.

Thanks for your input!
~MW

Issue · Github
by Sheila

Issue Number
1584
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
chandrans

Answers

  • GilHornungGilHornung Weizmann InstituteMember

    Hi,
    Not an "official" answer. But what I did was to refer to the OxoG paper:
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616734/

    I plotted my data similarly to Fig 9: TLOD vs FoxoG for C>A and G>T and for the rest of the mutations. Based on the figure I decided on thresholds. The suggestion in the paper is tumor_lod > −10 + (100/3) FoxoG.

    Happy new year

    Gil

  • mikawinmikawin Member

    Hi Gil,

    Thank you for your answer. I do have a couple of follow-up queries though:

    • What annotation do you actually set the threshold for?
    • If you do set it for the Tumor LOD score, do you do it for every position? [i.e. apply the formula tumor_lod > −10 + (100/3) FoxoG for every single value in the VCF file?]
    • Do you have an estimate of how many positions you filter out?

    Thanks for your input!

    Cheers,
    ~MW

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @mikawin @GilHornung
    Hi MW and Gil,

    You can have a look at the FireCloud website to see what the Cancer Group does. Thanks Gil for jumping in!

    -Sheila

  • mikawinmikawin Member

    Hi Sheila,

    I checked the Firecloud website and a query for FoxoG filters leads me back to this forum. Therefore can you elaborate further here on how the filter criteria should be applied.

    Thanks for your input!

    ~MW

    Issue · Github
    by Sheila

    Issue Number
    1627
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    vdauwera
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hey @mikawin, sorry for the game of circular pingpong. The fact of the matter is we don't have recommendations documented for this annotation; it's a metric that was developed by CGA as far as I know, and although we have taken ownership of the MuTect code itself, CGA still owns the downstream analysis, including filtering based on MuTect output. So if they don't have any documentation for this, nor any methods available in FireCloud that make use of it, there's really nothing we can do except recommend you ask the FireCloud team in the FireCloud forum, since they are responsible for answering exactly that sort of question.

  • mikawinmikawin Member

    @Geraldine_VdAuwera said:
    ... there's really nothing we can do except recommend you ask the FireCloud team in the FireCloud forum, since they are responsible for answering exactly that sort of question.

    Hey G,

    Thanks for your reply! Will post the query in the other forum.

    ~MW

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