Re: [galaxy-user] Samtools Mpileup output
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/
[galaxy-user] Samtools Mpileup output
Hi, I am using Mpileup from the Main Server (current version 0.0.1). In theory, this tool can generate two formats of output files: either a .bcf or a pileup. However, I couldn't find the option to select a .bcf file, even when I click on Set advanced options. When run, the program gives a pileup output format. Would you have any advice to select the output format, or alternatively, a tool in Galaxy that can convert pileup into .vcf? Many thanks for help, -- 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/
Re: [galaxy-user] Samtools Mpileup output
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 ___ 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/
