From 750ded30fa4e290abcfd6e37b8965a2604a86e8d Mon Sep 17 00:00:00 2001
From: "Jeroen F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Tue, 14 Feb 2017 17:02:13 +0100
Subject: [PATCH] Update notes_2017_02_14.md

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 notes/wd/notes_2017_01_31.md | 34 ----------------------------------
 notes/wd/notes_2017_02_14.md | 35 +++++++++++++++++++++++++++++++++++
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diff --git a/notes/wd/notes_2017_01_31.md b/notes/wd/notes_2017_01_31.md
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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
-Groningen).
-
-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
-Groningen.
-
-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
diff --git a/notes/wd/notes_2017_02_14.md b/notes/wd/notes_2017_02_14.md
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+# 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.
\ No newline at end of file
-- 
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