Tag Archives: variant calling

Poster about the EAGLE tool at University Hospital Essen Science Day 2015

Exome Analysis GraphicaL Environment (EAGLE)

Christopher Schröder, Christoph Stahl, Felix Mölder, André Janowicz, Jasmin Beygo, Marcel Martin, Sven Rahmanneagle

The Exome Analysis GraphicaL Environment (EAGLE) combines a best practices variant calling workflow, with a web frontend. By storing the called information in speficially structerd hdf5 files, EAGLE allows filtering and parameter tuning in almost real time. This enables iterative tuning of thresholds, or the selection of different samples for filtering by non computer scientists via the web interface.

Poster on Exomate at GfH 2014 in Essen

exomate-posterExomate: an easy to use exome sequencing analysis pipeline

Christopher Schröder, Johannes Köster, Christoph Stahl, Sebastian Venier, Sven Rahmann, Marcel Martin

Exomate is an exome-sequencing pipeline with a web frontend. It automates most steps needed to go from FASTQ files to variant calls, puts the calls and metadata about patients, samples, etc. into a database and then allows interactive analysis via a web frontend. It is primarily designed for easy use and has already been used in various studies [1,2,3].

[1] Martin, M. et al., 2013. Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3. Nat. Genet. 45, 933–936.

[2] Czeschik, J.C. et al., 2013. Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome. Hum. Genet. 132, 885–898.

[3] Voigt, C., et al., 2013. Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies – expanding the phenotypes associated with EFTUD2 hfg mutations.
Orphanet J Rare Dis 8, 110.