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data source questions

jmliucajmliuca Vancouver, CanadaMember

Hi
I am Jiaming Liu, research associate from Genetrack Biolabs, Canada. Our company is planning to setup Next Generation Sequencing system for genetic diseases and cancer gene testing. My job is to assess each platform and analysis software.
I am very interested in your alignment software. But I still have several questions need to be clarify:
1, for the reference sequences, do you pre-load them or we have to upload them? If you have pre-loaded reference sequences, how often you update the references?
2, for clinic mutation databases, how complete are they? how often do you update them? If possible, where your data sources are from, specifically, BRCA1, BRCA2...
3, if we have up-to-date databases, can we upload them and use them in this software?

After I receive your response, I will further discuss with you for more

Thanks
Jiaming Liu

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    Ah, yes you can use your own preferred mutation databases by specifying the relevant VCF files in your command line.

    To be clear, we don't currently provide an online GATK service where you would upload anything -- on this forum we just cover on-premise use of the GATK (eg if ypu're running on your own machines). There is a cloud-based cancer genome analysis service called FireCloud that can use GATK, and we are building a more general one (not focused on cancer) but support for that is provided at the link I referenced above.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there, I'm not sure what you're asking about. Are you asking this in relation to GATK, or something else? I'm asking because we don't make alignment software, we primarily make variant discovery software; and we don't (yet) provide a service for which pre-loading/uploading data sources would be relevant questions. If you're asking about FireCloud or Oncotator your questions might make more sense, but then you're not asking them in the right place... If you can please clarify I'd be happy to help direct you to the appropriate place.

  • jmliucajmliuca Vancouver, CanadaMember

    Sorry, I thought GATK was a alignment, variant calling and annotation software. My question is how you discover and annotate the variants. You must have a standard reference and clinic mutation database to compare with. So, how often you update your clinic mutation database? If we have a clinic mutation database, can we upload to the software? Thanks

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    Ah, yes you can use your own preferred mutation databases by specifying the relevant VCF files in your command line.

    To be clear, we don't currently provide an online GATK service where you would upload anything -- on this forum we just cover on-premise use of the GATK (eg if ypu're running on your own machines). There is a cloud-based cancer genome analysis service called FireCloud that can use GATK, and we are building a more general one (not focused on cancer) but support for that is provided at the link I referenced above.

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