Commit f87814e1 authored by Laros's avatar Laros

Update notes_2017_03_28.md

parent c8ee4dde
# Work discussion 14-02-2017
Present: Jonathan Vis (JV), Leon Mei (LM), Jeroen Laros (JL),
Pieter Neerincx (PN), Peter van 't Hof (PH), Gerben van der Vries (GV).
## GoNL re-analysis
Sample naming convention:
- We use the exising GoNL IDs that have no connection to biobanks.
- PhiX in the reference sequence. This was also asked in a VKGL meeting, there
was a preference to include it.
- Phase by transmission still needed, the haplotype caller does not take trio
date into account.
- Trio aware variant calling on one trio to compare to the haplotype caller.
Ansible installation testing is still needed. Especially the EasyBuild part is
challenging. PN and GV are going to do this.
10T reserved at the LUMC for this analysis.
## eLAN
Stress test still needed.
- Part of the GoNL project.
## CoManage
Authorisation workflow:
- Creating a VO succeeded.
- A lot of options, no good overview.
- PN suggests a hackathon (Gerben Venekamp, PN, Mark Santcroos) PN will
schedule this.
- Local enrollment, we first let UMCG and LUMC come up with solutions which we
will use as a template for other UMCs.
## Ansible and Easybuild integration
Usable at this moment.
- Nothing discussed about packaging.
- Ansible role working, needs to be documented.
- Ansible plugin is in the POC phase.
\ No newline at end of file
# Work discussion 14-02-2017
Present: Jonathan Vis (JV), Leon Mei (LM), Jeroen Laros (JL),
Mark Santcroos (MS), Pieter Neerincx (PN), Gerben van der Vries (GV),
Roan Kanninga (RK).
## GoNL re-analysis
Refset proposal:
- PN and JL are going to send this to the NCBI.
- The VKGL will be contacted for feedback.
RK: We should enable base recalibration.
- Can we use multiple recalibration files on the fly?
- If so, compare to the 'polished BAM' method.
QC:
- BAM statistics.
- Concordance with both array data and hg19-VCFs.
## eLAN
Test succeeded.
## CoManage
PN, MS, GV, Paul van Dijk had a hands-on session.
- Problems with the SQL database.
- An other meeting in April for an authorisation workflow.
- Before this, we need a test LDAP server in Groningen.
- MS has an LDAP server running, waiting for a firewall setting.
Rens (SURF) wants to test CoManage on the (new) BIOS VM.
## Ansible and Easybuild integration
Ansible installation testing:
- GV succeeded installing easybuild via ansible on Shark.
\ No newline at end of file
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment