Commit 6e9407de authored by Mei's avatar Mei
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Update notes_2017_04_11.md

parent 916d2403
......@@ -5,20 +5,10 @@ Mark Santcroos (MS), Pieter Neerincx (PN), Gerben van der Vries (GV),
Roan Kanninga (RK). Henk-Jan Zilverberg (HZ), Niels Idsinga (NI)
## 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.
GoNL spec
- GoNL spec will be freezed by Thursday. -
- QUAL in VCF? New QUAL introduced by GATK.
## eLAN
Resolved.
......@@ -33,8 +23,9 @@ PN, MS, GV, Paul van Dijk had a hands-on session.
- PN wanted to have a test/acc instance of IDP at Groningen for testing.
## Ansible and Easybuild integration
Ansible installation testing:
- GV succeeded installing easybuild via ansible on Shark.
- Gerben fixed the Molgenis-compute evn. Currently deployed at the home dir of Gerben. GV will deploy the env at bbmri-nl share.
- Pieter is improving the ansible playbook (replacing wget in shell with native Ansible commands).
- Pieter brought up an Ansible issue he encountered. Work around now by sourcing (e.g., bashrc) in Ansible. Because login shells of Ansible are not interactive. MS will check PN's
work around solution to see if it is reasonable.
## Virtual cluster setup at HPC Cloud (Mark)
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## Virtual cluster setup at HPC Cloud (MS)
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