[DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference

[Miguel Vazquez]

On Fri, Oct 7, 2016 at 10:37 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:

> Hi,
>
> Can someone give me an idea what the errors you see on real data are for
> Sanger?  Which real data is in use?
>

Junjun and I tried it on donor DO50398 and it failed on the pindel process.
I'll try to find our error report and forward it to you.


>
> Also what is non-standard in the BWA-mem preprocessing, I didn't work on
> the actual workflow but I did give input at the beginning (and have a very
> simple to use version in house which can run from fastq, BAM or CRAM
> inputs).
>

It seems to require removing the alignment of the BAM file or something
like that, right? I need to read more on it. Can you send me some info on
how you did it?

Best


>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
>
> kr2 at sanger.ac.uk
> Tel:+44 (0)1223 834244 Ext: 4983
> Office: H104
>
> On 7 Oct 2016, at 07:27, Miguel Vazquez <miguel.vazquez at cnio.es> wrote:
>
> Hi all,
>
> The Delly workflow on DO50311 just finished correctly. I've added that to
> the table. It's important to point out that I consider a success just that
> the workflow completes, not that the results are what they need to be. That
> I guess we can do at a later stage.
>
> By the way, the Delly workflow just seems to produce SV, is that the case?
> no SNV? It also produces a bedpe file that I guess I can try on the DKFZ,
> which is what was missing. I'm going to try that now, albeit with no clear
> idea of what I'm doing I must say, I'm not familiar with any of this.
>
> Current status so far as I understand it is that only Delly works straigh
> out of the box on real data, but only produces only SV. Sanger works on
> test data and fails on real data. DKFZ fails on Test data and requires
> bedpe file for real data (produced by Delly?) BWA-Mem requires preprocesing
> the files?
>
> I have to say that from where I stand the preprocesing required by Delly
> and BWA-Mem is a bit inconvenient and makes the tools not stand-alone.
>
>
> I admit that I'm not an expert so I might have got some info wrong. Any
> comments on this please?
>
> Best
>
> Miguel
>
>
>
> On Fri, Sep 30, 2016 at 3:52 PM, Francis Ouellette <francis at oicr.on.ca>
> wrote:
>
>> Dear Miguel and Junjun,
>>
>> Any more attempts on testing the PCAWG sanger docker container?
>>
>> If you reproduce the same error, we will need to involve Bryan and
>> Keiran Raine <kr2 at sanger.ac.uk> (author of the container).
>>
>> Let’s get this one figured out.
>>
>> I am going to assume that the making of the docker container is what
>> needs resolving.
>>
>> Brian: We may need your input here.
>>
>> Details of our current experiment should continue to be posted here:
>>
>> https://goo.gl/XX5BG9
>>
>> Thank you all,
>>
>> francis
>>
>> PS would be good for others on list to follow directions on above google
>> doc and also see if they can succeed on this workflow.
>>
>> Junjun and Miguel have tried different clouds, but used the sanger
>> workflow, on the same data set.
>>
>> Thank you for trying to do this.
>>
>> Would be good if I heard back from anybody before Monday AM (tech call).
>>
>> @bffo
>>
>> PS I CCed Keiran, but waiting to hear back from Brian before we need to
>> involve him some more.
>> PPS Junjun/Miguel: maybe you can try the DKFZ docker as well? (on the
>> same data set).
>>
>>
>> --
>> B.F. Francis Ouellette          http://oicr.on.ca/person/fran
>> cis-ouellette
>>
>>
>>
>> Begin forwarded message:
>>
>> *From: *Christina Yung <Christina.Yung at oicr.on.ca>
>> *Subject: **[PAWG-TECH] Draft agenda for PCAWG-TECH teleconference*
>> *Date: *September 30, 2016 at 9:19:39 AM EDT
>> *To: *"pawg-tech (pawg-tech at lists.icgc.org)" <pawg-tech at lists.icgc.org>
>>
>> Hi Everyone,
>>
>>
>>
>> Below is a draft agenda for Monday’s tech call.  Please let me know if
>> you have any agenda items for discussion.
>>
>> https://wiki.oicr.on.ca/display/PANCANCER/2016-10-03+PCAWG-
>> TECH+Teleconference
>>
>>
>>
>> Have a great weekend!
>>
>> Christina
>>
>>
>> Call Info
>>
>> *Usual Time            9 AM Eastern Time, Mondays*
>>
>> *UK                          0208 322 2500*
>>
>> *Canada                  1-866-220-6419*
>>
>> *United States        **1-877-420-0272*
>>
>> *All Others              Please see attached PDF file
>> <https://wiki.oicr.on.ca/download/attachments/57776990/PAWG-TECH-Telecon-International-Numbers.pdf?version=1&modificationDate=1401456003000&api=v2> with
>> a list of numbers for other countries.*
>>
>> *Participant Code  5910819#*
>> Agenda
>>
>>
>> *Time*
>>
>> *Item*
>>
>> *Who*
>>
>> *Attachments/Links*
>>
>> 5min
>>
>> Welcome. Wait for group members to log on
>>
>> Christina Yung <https://wiki.oicr.on.ca/display/%7Ecyung>, OICR
>>
>> 10min
>>
>> Overall status
>> Christina Yung <https://wiki.oicr.on.ca/display/%7Ecyung>, OICR
>>
>> ·         Linkouts to Most Current PCAWG Data
>> <https://wiki.oicr.on.ca/display/PANCANCER/Linkouts+to+Most+Current+PCAWG+Data>
>>
>> ·         Report data issues to pcawg-data at icgc.org, GNOS issue to:
>> Help at annaisystems.com
>>
>> ·         From Boston F2F: PCAWG datasets & dependencies
>> <https://docs.google.com/spreadsheets/d/1VltMMLL5XDIFipM3zzLqZOGj5z-UxIMKLDbsuDiD2Q8/edit?usp=sharing>
>>
>> *Action Items*
>>
>> 1.       [Joachim] Consensus SV - final?
>>
>> 2.       [Jakob] Consensus SNVs - changes to "SNV near indels"
>> annotation?
>>
>> 3.       [Junjun] Specimen ID mapping for miRNA and methylation
>>
>> 4.       [Jonathan & Joachim] Consensus calls for cell lines, followed
>> by filtering
>>
>> 5.       [Matthias & Gordon] Docker containers for filtering methods
>>
>> 6.       [Christina] Run alignment & variant workflows on
>> medulloblastoma sample (tumor 40x, normal 30x) from ICGC benchmark to
>> estimate false negative rate
>>
>> 7.       [Christina] Follow up with institutes interested in hosting
>> PCAWG data long-term
>>
>> 8.       [All] As per Jennifer's email on Sept 16, please provide
>> authorship information again or for the first time using PCAWG Author Form (
>> http://goo.gl/forms/5Wq5x5X1DK). Save the link "Edit your response" so
>> you can go back later to provide updates, for example about your evolving
>> role in writing specific papers.
>>
>> 9.       [All] Contribute to the manuscripts on
>>
>> a.       infrastructure: https://docs.google.com/docume
>> nt/d/10alAxrWLdLSyhci-rfNuVH13rFXCJkaY_rzf1KJn7nc/edit
>>
>> b.       variants: Paper ( https://goo.gl/g9CLsu ), Supplement (
>> https://goo.gl/EWYh7e )
>>
>> c.       Rogue's Gallery of Cancer Genome Sequencing Artifacts ( outline
>> <https://wiki.oicr.on.ca/download/attachments/66958609/Rogues%E2%80%99%20Gallery%20of%20Cancer%20Genome%20Sequencing%20Artefacts.pdf?version=1&modificationDate=1469802643000&api=v2>
>> )
>>
>> 10.   [Junjun] Discuss PCAWG vs DCC glossary terms at next PCAWG-10/13
>> conference
>>
>> 10min
>>
>> Status of dockerizing workflows
>> Brian O'Connor <https://wiki.oicr.on.ca/display/%7Eboconnor>, UCSC
>>
>> Gordon Saksena
>> <https://wiki.oicr.on.ca/display/%7Egsaksena@broadinstitute.org>, Broad
>>
>> Francis Ouellette <https://wiki.oicr.on.ca/display/%7Efrancis>, OICR
>> *Status of PCAWG Workflow ports to Dockstore*:
>>
>> Denis has been porting the Dockstore entries to CWL version 1.0 which is
>> part of our effort to publish Dockstore (this doesn't affect the content of
>> the pipelines, simply their "descriptors" which allow them to be runnable
>> via Dockstore). Denis has also worked on testing BWA-Mem, Sanger, EMBL
>> (which all work with CWL 1.0 and Kerian's test dataset) and has fixed
>> issues with DKFZ and is testing the latter with a real sample shortly.
>>
>> 1.       BWA-Mem - Ready for testing by Francis' team
>>
>> 2.       Sanger - Ready for testing by Francis' team.
>>
>> 3.       EMBL - Ready for testing by Francis' team.
>>
>> 4.       DKFZ - Ready for testing by Francis' team. I've exchanged
>> emails with Manuel Ballesteros who has been testing this pipeline.
>>
>> 5.       Broad - Variant calling (MuTect, dRanger, snowman), need some
>> work, Gordan sent details previously
>>
>> 6.       OxoG - Waiting for Dimitri to provide OxoG docker
>>
>> 7.       Variantbam
>>
>> 8.       Consensus algorithm
>>
>> PCAWG Docker (Dockstore) Testing Working Group
>> <https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+Docker+%28Dockstore%29+Testing+Working+Group>
>>
>> 5min
>>
>> Other business?
>>
>> Group
>>
>>
>>
>>
>>
>>
>>
>> *Christina K. Yung, PhD*
>> Project Manager, Cancer Genome Collaboratory
>>
>> *Ontario Institute for Cancer Research*
>> MaRS Centre
>>
>> 661 University Avenue, Suite 510
>> Toronto, Ontario, Canada M5G 0A3
>> Tel: 416-673-8578
>>
>> www.oicr.on.ca
>>
>>
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>
>
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