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.


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
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