Boston College Collaboration

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Working with Boston College

Goals[edit]

  • generate a set of pipelines
    • sequence alignment
    • variant calling
    • association analysis
  • Easy for non-expert to use
  • Make available on a cloud (Galaxy)

Tasks[edit]

Task Deadline Assignee Status
Assign each tool a project "point person" DONE June 13, 2012 Everyone Done

SeqShop[edit]

Meetings[edit]

We will have bi-weekly meetings about this collaboration.



Tools[edit]

UM Tools to include in the Launcher/Pipelines[edit]

  • QPLOT - Xiaowei
  • glfMultiples - TBD - Goncalo & Hyun need to make sure their latest are merged
  • polymutt - Bingshan
  • clipOverlap - Mary Kate
  • VerifyBamID - Hyun
  • trioCallerVCF - Wei
    • Only downloads of the binary are available. Wei said to let him know when we need the source code.
  • anno - Xiaowei
    • (the updated vcfCodingSnps) documentation is not yet external
  • thunderVCF - Xiaowei may have some updates
    • need to find the latest documentation/download and update with the parameters.
  • Deduper/Recalibrator - Mary Kate
    • I'm almost done this, but need to cleanup the options, document, test, and enhance the recalibrator.
    • Recalibration Timing
  • UMAKE - Goo & Hyun
    • Documentation will be updated when the new version is released

External Tools[edit]

  • samtools-hybrid (Needs to be documented) - Mary Kate
  • SVM filter (need to check copyright on this) - Goo

Additional tools that could potentially be included[edit]