[Geuvadis_rna_analysis] Geuvadis updates from Cold Spring Harbor

Hello all, Greetings from Cold Spring Harbor! The Geuvadis RNAseq poster was really popular and lots of people were impressed by the dataset and the analyses that we put together for the poster. There is definitely a lot of interest in the paper and the dataset. Now that there are so many people waiting for the paper and the data to come out, let's keep on working to make sure we'll get it done sooner rather than later. A couple of questions/issues: - FYI to everyone, the GEM manuscript is still not submitted despite many promises to get it done by the end of April. - Micha/Thasso, what's the situation regarding the gem-bam conversions? Are you running them and if not, can you start asap? We need to make sure that if the manuscript gets submitted and we can decide to use GEM (I wish that this was a question of when and not if), there's no delay from this. - genotype data of the Phase2 samples: I talked with Bryan Howie (developer of IMPUTE2), and he said that including rare variants and indels in the reference panel should be fine. Natalja/Thomas, am I correct that we already had chr1 results where imputation was done with the full Phase2 set + the total Phase1 without any additional variant filters, and this looked pretty good? On another note, I learned that the Phase2 genotype calls are almost there - I'm discussing with people from the Broad if we could use them and if that would give us better data than imputing. cheers, 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(a)unige.ch