SomaticIndelDetector is deprecated ??

sbahetisbaheti Posts: 18Member

Hi

I am using the latest version of GATK 2.4.9 and i don't find the Somatic Indel Detector walker
java -jar GenomeAnalysisTK.jar -T SomaticIndelDetector -h

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.4-9-g532efad):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: SomaticIndelDetector
ERROR ------------------------------------------------------------------------------------------

Is this walker is not supported any more.

Thanks
Saurabh

Best Answer

Answers

  • zhouyunyun11zhouyunyun11 Posts: 1Member

    MuTect is used to detect the point somatic mutation. Since SomaticIndelDetector has been removed, how can I find the somatic indels? Do you know where can I find this program? Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,365Administrator, GATK Developer admin

    Hi @zhouyunyun11, please see the accepted answer -- please contact the Broad cancer group.

    Geraldine Van der Auwera, PhD

  • YujianYujian Posts: 6Member

    Could you recommend any software from Broad Cancer Group?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,365Administrator, GATK Developer admin

    The simplest way to get answers about this is to ask this question in the MuTect section. MuTect is produced by the Cancer Group so they will know.

    Geraldine Van der Auwera, PhD

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