Hi Carlos, Thanks for your help: setting "Genotype Likelihood Computation" to "Perform genotype likelihood computation" do give a bcf in output rather that a pileup. Then I use "bcftools view" to convert this bcf to a standard vcf format.
Fabrice Le 06/11/2013 20:32, Carlos Borroto a écrit : > On Wed, Nov 6, 2013 at 12:08 PM, Fabrice Besnard > <fbesn...@biologie.ens.fr> wrote: > >> Would you have any advice to select the output format, or alternatively, >> a tool in Galaxy that can convert pileup into .vcf? >> > > Hi Fabrice, > > I believe you only get the BCF output when "Genotype Likelihood > Computation" is set to "Perform genotype likelihood computation". > > Hope it helps, > Carlos > -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesn...@biologie.ens.fr Tel: +33-1-44-32-39-31 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
