Commit 750ded30 authored by Laros's avatar Laros
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# Work discussion 31-01-2017
Present: Jonathan Vis (JV), Leon Mei (LM), Jeroen Laros (JL),
Pieter Neerincx (PN)
Starting Feb 1 Mark Santcroos will start in Leiden.
## eLAN
Operational between Surf, Leiden and Groningen (pinging works from Leiden to
Now a stress test should be conducted; random data (small and large files)
and/or data from the BIOS project.
## CoManage
CoManage is set-up at Surf and is ready for testing.
PN likes to use CoManage for account management on the newly ordered cluster in
PN wants to build an authorization workflow in CoManage.
## Re-run GONL
PN will recreate the workflow. Use GONL as a reference set for variant liftover
from build 37 to build 38.
## Ansible and Easybuild integration
LM proposes a hands-on session in February (week of the 20th).
Build the dependency graphs for molgenis compute and biopet.
March 16 meeting at Surf
# 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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