[DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference
Francis Ouellette
francis at oicr.on.ca
Fri Dec 9 14:46:31 EST 2016
Please e-mail Miguel( and/or this list) if there are any docktesting updates before Monday.
I will not be on pcawg-tech call, but Miguel will be.
https://wiki.oicr.on.ca/display/PANCANCER/2016-12-12+PCAWG-TECH+Teleconference
Have a great weekend,
@bffo
--
B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette
Begin forwarded message:
From: Christina Yung <Christina.Yung at oicr.on.ca<mailto:Christina.Yung at oicr.on.ca>>
Subject: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference
Date: December 9, 2016 at 2:40:11 PM EST
To: "pawg-tech (pawg-tech at lists.icgc.org<mailto:pawg-tech at lists.icgc.org>)" <pawg-tech at lists.icgc.org<mailto:pawg-tech at lists.icgc.org>>
Hi Everyone,
Below is a draft agenda for Monday’s tech call. Please feel free to edit on the wiki:
https://wiki.oicr.on.ca/display/PANCANCER/2016-12-12+PCAWG-TECH+Teleconference
Best regards,
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/~cyung>, OICR
10min
Overall status
Christina Yung<https://wiki.oicr.on.ca/display/~cyung>, 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<mailto:pcawg-data at icgc.org>, GNOS issue to: Help at annaisystems.com<mailto:Help at annaisystems.com>
• From Boston F2F: PCAWG datasets & dependencies<https://docs.google.com/spreadsheets/d/1VltMMLL5XDIFipM3zzLqZOGj5z-UxIMKLDbsuDiD2Q8/edit?usp=sharing>
Action Items
1. [Junjun] Specimen ID mapping for miRNA and methylation, see update below:
a. miRNA release posted in Linkouts to Most Current PCAWG Data<https://wiki.oicr.on.ca/display/PANCANCER/Linkouts+to+Most+Current+PCAWG+Data> item #11.
i. Release table includes various entity IDs, source miRNA data, and mapping between miRNA samples and WGS / RNA-Seq samples, Google Spreadsheet: https://docs.google.com/spreadsheets/d/1QG8UTaX71H6tpvt-XJp0_pGFkxURWZ8tC1cIMg3sMJM/edit#gid=2063341485
ii. The release is also available here in TSV, JSONL formats (easy for programmatic parsing):
• http://pancancer.info/data_releases/mirna/mirna_release.v1.0.jsonl
• http://pancancer.info/data_releases/mirna/mirna_release.v1.0.tsv
• http://pancancer.info/data_releases/mirna/mirna_sample_sheet.v1.0.tsv
b. New RNA expression data file produced, previously reported issue about missing aliquot fixed.
c. Methylation WG will have have first complete set of analysis result by mid December. Will wait till then to revisit the matching of sample IDs.
2. [Junjun] Create directories on ICGC Portal for reference datasets, see update below:
a. Reference data folder structure reorganized available at https://dcc.icgc.org/releases/PCAWG (README under each sub-folder will be added to provide addition information).
PCAWG
└── reference_data
├── data_for_testing
├── pcawg-broad
├── pcawg-bwa-mem
├── pcawg-delly
└── pcawg-sanger
b.
c. Other additional reference data from other working groups can be added too.
• hg19_cosmic_v54_120711.vcf - Adam Butler confirmed that this file can be redistrubted with the other references files used by Broad.
3. [Jonathan] For cell lines, consensus SVs available: pdf<https://www.dropbox.com/s/tbchodphnanusv3/20161017_pcawg_cell_line_sv_jweischenfeldt.pdf?dl=0>; syn7373725<https://www.synapse.org/#!Synapse:syn7373725>. Consensus SNVs & indels:
. merged results passed to Broad for filtering
a. dkfz-filtered SNVs have been added to https://www.synapse.org/#!Synapse:syn7510859<https://www.synapse.org/#%21Synapse:syn7510859>
4. [Christina] For medulloblastoma sample (tumor 40x, normal 30x) from ICGC benchmark, run alignment & variant workflows
. Sanger - completed
a. DKFZ/EMBL - Encountered 2nd Roddy error. Logs sent to Michael.
b. Broad v1 completed - passed to Broad to fix
5. [All] Contribute to the manuscripts
. infrastructure: Paper ( https://goo.gl/utx3cC ), Supplement ( https://goo.gl/gtYUv7 )
a. variants: Paper ( https://goo.gl/g9CLsu ), Supplement ( https://goo.gl/EWYh7e )
b. 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> )
i. some examples from Matthias: GroupSeminar_20160531_onlyPCAWG.pptx<https://wiki.oicr.on.ca/download/attachments/67770698/GroupSeminar_20160531_onlyPCAWG.pptx?version=1&modificationDate=1475242901000&api=v2>
• Nuno just reported 7 whitelisted aliquots are missing from V1.6 of consensus SV. Joachim explained that 1 of the 4 SV callers failed for these aliquots, and has added a note to Synapse.
15min
Update on publication plan
Lincoln Stein<https://wiki.oicr.on.ca/display/~lstein>, OICR
10min
Status of dockerizing workflows
Denis Yuen<https://wiki.oicr.on.ca/display/~dyuen>, OICR
Brian O'Connor<https://wiki.oicr.on.ca/display/~boconnor>, UCSC
Gordon Saksena<https://wiki.oicr.on.ca/display/~gsaksena@broadinstitute.org>, Broad
Status of PCAWG Workflow ports to Dockstore:
1. [Kyle] MuSE
2. [Gordon] Broad dockers with #days estimated for development
a. 0 - tokens alg, for SNV/Indel PoN generation (not GATK)
b. 5 - SNV/Indel PoN filter
c. 3 - MuTect with ContEst wiring bug, plus rescue, plus SV minibam, using public PoN (GATK)
d. 3 - MuTect without ContEst wiring bug, using public PoN. (GATK license)
e. ? - MuTect PoN generator
f. 3 - OxoQ measure + OxoG filter (GATK license due to filter step)
g. 5 - Snowman (GPL needs to be unlinked. not GATK)
h. 5 - dRanger, includes preprocess and BreakPointer. (does public PoN exist? release without PoN?)
i. ? - dRanger PoN generator
j. 3 - frag counter
k. 3 - haplotype caller (GATK)
l. 3 - RECapseg (GATK)
m. 3 - vcf merge (GATK)
n. ? - het sites force call (GATK, results never used due to bug)
o. ? - BQSR + cocleaning (relying on Kyle)
p. 10 - deTiN - detection and filter (GATK)
q. 3 - gVCF merge (GATK)
r. 5 - blat SNV filter (GATK)
s. 10 - germline overlap SNV filter (GATK)
t. ? - Variantbam
3. [Jonathan] Consensus algorithm for SNVs: 2+ of 4
4. [Jonathan] Consensus algorithm for indels: stacked logistic regression - Update from Jonathan on 11/22: 1 week to work on scripts, 1.5 week to Dockerize
5. [Joachim] Consensus algorithm for SVs - will check in on 12/5
Of note:
• Naming convention: "pcawg-<name>-workflow" for complex, docker-based workflows; or "pcawg-<name>-tool" for standalone, single tools
• currently working on releases using gosu to tackle "unknown user issue" and new test.json pointing at pcawg site
• PCAWG DOI Generation<https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+DOI+Generation> for a howto guide on doing this (we use GitHub + Zenodo)
• Brian's Dockstore tutorials:
• https://www.youtube.com/watch?v=sInP-ByF9xU
• https://www.youtube.com/edit?video_id=-JuKsSQja3g
• Tutorial from 12/6: https://goo.gl/2bnXq<https://goo.gl/2bnXqs> & https://www.youtube.com/watch?v=Gb6LnmpZj_g
10min
Status of testing dockerized workflows
Francis Ouellette<https://wiki.oicr.on.ca/display/~francis>, OICR
Denis Yuen<https://wiki.oicr.on.ca/display/~dyuen>, OICR
Brian O'Connor<https://wiki.oicr.on.ca/display/~boconnor>, UCSC
PCAWG Docker (Dockstore) Testing Working Group<https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+Docker+%28Dockstore%29+Testing+Working+Group>
Workflow Testing Data<https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data>
Docker containers to be tested<https://wiki.oicr.on.ca/display/PANCANCER/Docker+containers+to+be+tested>
________________________________
Copy of table from "Workflow Testing Data<https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data>" representing latest status of PCAWG docker
containers currentlt present on the PUBLIC Dockstore.org<http://dockstore.org/> and what the status of their testing is (taken 08:30 AM EDT, Dec 5, 2017).
[cid:image001.png at 01D2522A.2678F110]
________________________________
Status of workflows being tested:
1. BWA-Mem
2. Sanger - Changes proposed by Keiran have been made. Currently testing if the new version fixes issues with a specific donor (DO50311); test had to be restarted due to reboot for security patch
a. Tests passed with 2.0.2, watch out though, test data ran at the regular time, but the previously failing donor DO50311 took upward of 8 days
3. EMBL
4. DKFZ
5. DKFZ's PCR & strand bias filtering
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<http://www.oicr.on.ca/>
www.cancercollaboratory.org<http://www.cancercollaboratory.org/>
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