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 |
---|---|---|---|
June 13, 2012 | Everyone | Done |
SeqShop[edit]
Meetings[edit]
We will have bi-weekly meetings about this collaboration.
- GotCloud Internal Meeting March 9, 2015
- GotCloud Internal Meeting March 2, 2015
- GotCloud Internal Meeting February 16, 2015
- GotCloud Internal Meeting January 26, 2015
- GotCloud Internal Meeting January 19, 2015
- GotCloud Internal Meeting January 12, 2015
- GotCloud Internal Meeting December 1, 2014
- GotCloud Internal Meeting November 24, 2014
- GotCloud Internal Meeting November 17, 2014
- GotCloud Internal Meeting November 3, 2014
- GotCloud Internal Meeting October 27, 2014
- GotCloud Internal Meeting October 6, 2014
- GotCloud Internal Meeting October 1, 2014
- GotCloud Internal Meeting September 22, 2014
- GotCloud Internal Meeting September 15, 2014
- GotCloud Internal Meeting September 11, 2014
- GotCloud Internal Meeting September 2, 2014
- GotCloud Internal Meeting August 26, 2014
- GotCloud Internal Meeting August 4, 2014
- GotCloud Internal Meeting July 28, 2014
- GotCloud Internal Meeting July 14, 2014
- GotCloud Internal Meeting July 7, 2014
- GotCloud Internal Meeting June 30, 2014
- GotCloud Internal Meeting June 2, 2014
- GotCloud Internal Meeting May 19, 2014
- GotCloud Internal Meeting April 14, 2014
- GotCloud Internal Meeting March 24, 2014
- GotCloud Internal Meeting February 24, 2014
- GotCloud Internal Meeting February 17, 2014
- GotCloud Internal Meeting February 10, 2014
- GotCloud Call with BC February 3, 2014
- GotCloud Internal Meeting January 27, 2014
- GotCloud Internal Meeting January 20, 2014
- GotCloud Internal Meeting December 10, 2013
- GotCloud Internal Meeting December 3, 2013
- GotCloud Internal Meeting November 26, 2013
- GotCloud Internal Meeting November 19, 2013
- GotCloud Internal Meeting October 29, 2013
- GotCloud Internal Meeting October 15, 2013
- GotCloud Internal Meeting September 17, 2013
- GotCloud Internal Meeting Aug 12, 2013
- GotCloud Internal Meeting May 13, 2013
- GotCloud Internal Meeting April 8, 2013
- GotCloud Internal Meeting February 18, 2013
- BCUM Internal Meeting October 22, 2012
- BCUM Internal Meeting October 8, 2012
- NHGRI Sequencing Network Meeting October 1, 2012 - Houston, TX
- BCUM Teleconference September 25, 2012 - Discussion of Presentation for Oct 1
- BCUM Teleconference September 19, 2012
- BCUM Internal Meeting September 17, 2012
- BCUM Teleconference September 4, 2012
- BCUM Internal Meeting August 22, 2012 - Overview of alignment pipeline setup
- BCUM Teleconference August 14, 2012
- BCUM Internal Meeting August 1, 2012
- BCUM Teleconference July 24, 2012
- BCUM Internal Meeting July 18, 2012
- BCUM Internal Meeting June 27, 2012
- BCUM Internal Meeting June 13, 2012
- BCUM Internal Meeting May 25, 2012
- BCUM Collaboration Meeting in Boston April 2, 2012
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]
- EMMAX
- needs to be released and public documentation provided
- LocusZoom