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 <fbesnard@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: fbesnard@biologie.ens.fr Tel: +33-1-44-32-39-31