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Posters on somatic analysis with GATK4 presented at AACR 2017

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited April 2017 in Announcements

A few of us GATKers (among a flood of other Broadies) traveled to Washington, DC this week for the General Meeting of the American Association for Cancer Research (AACR). Here are PDF copies of the posters we presented on Tuesday morning.

Abbreviated title Presenter Link
Somatic mutation discovery with GATK4 Geraldine Van der Auwera PDF
Allelic Copy Number Variation Discovery Aaron Chevalier PDF
Copy Number Variation Discovery in WGS and Exomes Mehrtash Babadi PDF

Incidentally, it's the end of the conference so now 10,000 people are trying to get home, and apparently half of them are going to Boston. I was hoping to catch an earlier flight on standby; the gate attendant laughed so hard. Most of the flights are overbooked to start with. So I have some time to kill until 9 PM. Well, I guess there's plenty of documentation in need of writing!

Comments

  • sebastian_dsebastian_d Member

    Thanks for sharing!

  • jcorominasjcorominas RadboudumcMember

    Dear Geraldine Van der Auwera,
    I found the poster (Copy Number Variation Discovery in WGS and Exomes) presented in AACR 2017 really interesting, together with the talk that Mertash Babadi did on the MIA (March 15, 2017) about "A scalable Bayesian framework for inferring copy number variation". I would love to try this tool, for that reason I would like to ask if the tool GATK gCNV will be available to the rest of the scientific community, and if so when we can expect it.
    Looking forward to hearing from you.
    Best wishes,
    Jordi Corominas Galbany

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @jcorominas, the software is already available as an alpha preview and will be released in beta status sometime next month. We don't have much documentation on it yet but if you post questions in this forum the developers will help you get started.

  • jcorominasjcorominas RadboudumcMember

    Thank you very much! Do you know if it's possible to run it on whole genome data for germline CNVs?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I think it is, though I'm not sure what the performance looks like. We'll get you answers in the alpha forum.

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