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OxoGmetrics task in GATK not found

ncamardancamarda DFCIMember, Broadie
edited March 2017 in Ask the GATK team

Hello,
I am trying run the OxoGMetrics task according to the following command (which I found in the Firehose task registry):

java -Xmx2g -jar /GenomeAnalysisTK.jar --analysis_type OxoGMetrics -R -I -L -o

and I'm realizing that this task doesn't exist in the current GATK framework (3.7). Supposedly this task was written / updated last in 2012 so I went back and compiled the version of GATK at the time (1.6). I checked the available tasks for this version of GATK and OxoGMetrics is still not included.

I've tried running the picard version of this task but the output headers are incompatible with the "append OxoG" step.

I'm clearly missing something here and could use some advice on how to run this part of the OxoG workflow. Thank you so much.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there, if you're referring to the CollectOxoGMetrics tool it's in Picard, not GATK.

  • ncamardancamarda DFCIMember, Broadie
    edited March 2017

    Sorry Geraldine, I just updated my post -- I've tried this Picard Tool and the output is in an entirely different format from what the downstream "append OxoG" task is expecting, and there doesn't seem to be a straight-forward way to make them compatible

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @ncamarda,

    Check out GATK's OxoGReadCounts module. Looks like it can only be called from MuTect2, which is a tool that is in beta. So annotating with this metric is coupled to calling variants with MuTect2, which is not ready for production use.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Oh my bad, I wasn't up to date on the somatic GATK tools. This is an area of intense development right now. We're porting functionality that was developed by CGA in separate codebases (often one-offs per-tool) into the GATK codebase, but a lot of that is not yet available through our tools yet. You may have better luck asking the CGA team in the FireCloud forum.

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