Version 1 (modified by Morris Swertz, 11 years ago) (diff)


GoNL Analysis Call 2011-09-07

Attending: Pieter, Morris, Barbera, Kai, David, Victor, Martijn, Slavik, Alex, Elisa, Eric-Wubbo, Freerk, Leon

Presentation of SNP was postponed as Laurent and Paul where not there.

Action list

ongoing ==

  • (new) morris: organize data access elisa, kai
  • We need to start drafting the validation experiments! (Morris/Paul?? need to add section to SV plan so we can come up with one validation plan).
  • Morris will update alignment progress report again
  • Jan and Pieter will sent the SV BAM files first to the SARA grid
  • We complete SNP pilot2 and add the SV samples to SNP pilot3 (16 trios, 4 quarted)
  • Leon and Jeroen will draft request to GoNL whether can DVD use the GoNL data

done since last week

  • Jeroen and Morris will exchange data models for DVD

Upcoming presentations

  • Imputation team will report progress next week
  • SV team will report progress next week
  • Laurent will present first results of 51 trios, date to be decided.

Update alignment 2.0

Pieter: Still running.

Update alignment 1.0


  • batch3 done, except 1 flowcel (second end doens't look good)
  • batch4 ongoing
  • batch5 started
  • batch6 done.


  • batch2, 2 lanes that need to be markduplicates. 83 %.
  • Barbera will contact Jan en Tom for the


  • done with lane analysis. Transfer data back. 50TB.
  • Barbera.

Update from SV team

Eric-Wubbo: Run pindel on 50 samples. Takes 48 cpu days on groningen cluster. Now counting number of indels/deletions. 20Gb/thread. Still optimizing for maximum memory usage.

Victor: 1-2-3sv through phase 1, found problematic regions. Now on phase 2, cluster. By end of week can do comparison. Also made primers for new segments found in A4 trio. Wigard going to verify.

Joep: Can not run Breakdancer. Some Perl modules are missing.

Slavik: Annotation pipeline for breakseq. Some on annotation only on subscription but slowly progressing and in a few weeks will have annotation pipeline. Then question: which data sets to use.

Abishek: Missed last telco. Denovo assembly together with Victor. Using different tool. Abi using Abyss, we using Soapdenovo. Also talking to ben turner and include newest CLC version.


  • David can share script with Eric-Wubbo to monitor.
  • Pieter will pick up on the Perl problems.


  • face2face meeting in Utrecht, thursday afternoon.



  • how to get access to reference genomes.

See Morris will provide data access

  • will run imputation procedure over the weekend
  • next call tomorrow, also define pipeline for GRID testing

Data access