GATK test data for Mutect?

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registered_user

• April 29, 2024 08:55

Am I correct that there exists no tumor-normal pairs of bams for testing Mutect at the GATK Test Data repository, or am I just not finding the data? (https://s3.amazonaws.com/gatk-test-data/gatk-test-data-readme.html)

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  Gökalp Çelik

  • April 29, 2024 12:54

  Hi

  We don't have any such data but you are free to use tools to generate simulated data for this purpose. 

  https://academic.oup.com/narcancer/article/5/3/zcad051/7280539 

  https://github.com/BrianOSullivanGit/stochasticSim 

  Though we do not provide any support for such tools I believe this would help you tune up your parameters. 

  Regards. 

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