Hello all,

Here are the minutes of the Geuvadis analysis group TC of May 17th.

The next call will be in one week, May 24 at 2pm CET.

- The analysis group meeting in July will be 1.5 days from Monday noon to Tuesday late afternoon. Gabrielle will set up a registration page and sort out practicalities.
- The last round of Kiel miRNAs are getting sequenced next week
- GEM submission is a few days away. Bams are uploading and will be all on the ftp site by the end of the week.
- Allelic mapping bias simulations from Tuuli should run it with GEM. It will be lots of reads to map, according to Micha they can do it within a month.
- EBV quantifications with GEM are done, and Micha will see that they get uploaded to the ftp site
- There has been some progress in imputations, we should have results by the end of the month (although some more issues were discovered after the call...)
- Tuuli got some QC updates from Uppsala, and we'll work to get the final the QC done (samples to exclude) by the end of the month, and normalization of quantifications (for eQTL and other such analyses) by early June
- Splice junctions: Pedro/Jean can start running their exon inclusion/exclusion stats once the GEM bams are available, and Micha is working on split read quantifications
- The first version of variant annotations is on the ftp site (an extension from 1000g annotations). By next week we should put together a list of what kind of categories we want to have in the final version.
- Henk and Marc are working on refining miRNA annotation, and after that is done Marc has a bunch of analyses planned
- Manny has been working on NMD deficiency, and is planning a LOF subgroup call for next week

best regards,
Tuuli


Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University of Geneva Medical School
CMU / Rue Michel-Servet 1
1211 Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen@unige.ch

On 5/16/12 2:17 PM, Tuuli Lappalainen wrote:
Hello,

We'll have a Geuvadis analysis group TC on Thursday the 17th at 2pm CET. I know this is a public holiday in many countries, but I'd prefer having the call anyway with those of you who can attend, it's been a while.

Things to discuss:
- updates from GEM submission and bams, QC, and imputation
- reference allele mapping bias simulations for GEM
- next steps in analysis:
    - eQTL tests
    - splice junction quantifications
    - variant annotation categories
    - miRNA
    - loss-of-function
    - others?
- July meeting practicalities

The numbers are:
from outside spain; 0034917911859
from spain; 900800678
Access code; 3160100


-- 
Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University of Geneva Medical School
CMU / Rue Michel-Servet 1
1211 Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen@unige.ch