Commit c8ee4dde authored by Laros's avatar Laros

Notes 28-02-2017.

parent 750ded30
# Work discussion 14-02-2017
Present: Jonathan Vis (JV), Leon Mei (LM), Jeroen Laros (JL),
Pieter Neerincx (PN), Sander Bollen (SB), Peter van 't Hof (PH),
Mark Santcroos (MS), Roan Kanninga (RK), Irene Nooren (IN),
Stefan van Aalst (SA).
## GoNL re-analysis
[Notes]() from PH:
- We use GRCh38 without alternative loci, including decoys. PH will check
whether unplaced contigs are present.
- Discussion about changing the reference (inclusing PhiX). Apparently needed
for GoNL (no barcoding), but changing the reference causes other problems.
We postpone this discussion.
- Workflow: Trio aware variant calling? Is the current calling in GATK
comparable to the trio aware calling?
- Indel realignment?
- Imputation, we decide this after we get te gVCF files.
- Concordance checks with arrays.
- Contamination checks.
- Computation: about half in Groningen, half in Leiden. Also a small batch at
SURF. Proposal: do the first batch on all locations.
- Molgenis compute as framework.
## eLAN
No time for updates.
- Stress test still needed.
## CoManage
No time for updates.
## Ansible and Easybuild integration
No updates.
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# 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.
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