Re: [galaxy-user] SnpEff on Main
Hi Sathya, The SnpEff tool is set up at this time for annotation with the /C. elegans/ WS220 genome only. Including human in the future on the public Main server at http://usegalaxy.org is under current evaluation. For now, use the tool in a local or cloud Galaxy instance, with the tool installed from the Tool Shed. Help to get started can be found here: http://getgalaxy.org http://usegalaxy.org/cloud http://usegalaxy.org/toolshed Take care, Jen Galaxy team On 3/12/14 1:44 AM, Sathya wrote: I am working on the project to predict SNP from NGS data. I have found SNP using SAM tools and GATK (used reference hg19). I would like to know effect of SNP using SNPeff in GALAXY. I have given SNP in vcf format. I could not change the genome option as human, it is set is C.elegans by default Please help me to solve this ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server atusegalaxy.org http://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/ -- With regards, Sathya.B ___ 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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] SNPeff on human genome
Hello, SNPEff is available for use with the human reference genome in the GATK pipeline (the 1000 genomes version, called Homo sapiens b37 (hg_g1k_v37) in Galaxy). See the tool NGS: GATK Tools (beta) - Variant Annotator and look in the list of Annotations to apply. The best documentation is at the GATK web site itself - we do not have extra tutorials available at this time (tools are still technically in 'beta'). Following the links on the tool forms for help are a start, but with the updated documentation structure they point to, it can be confusing. So, I pulled out the a relevant link that I think would be a good place to start, to learn more about this function (I just used the search function on the tool name, you could do same to explore other related info). You can also search for information about the genome source (obtained from GATK bundle last May). http://gatkforums.broadinstitute.org/discussion/50/adding-genomic-annotations-using-snpeff-and-variantannotator Please note that the version of the genome you use very much matters with these tools - hg19 and hg_g1k_v37 are the same genome release, but differ in small ways when it comes to chromosome naming and some other organization (if using hg19 full). This can make it a tedious challenge to lift data between the two - we won't be able to help except with general guidelines - and the tools will not function if incorrect. SO - the absolute top advice I can give you is to pick a genome and stick with it throughout your entire analysis to avoid issues. If you plan to use GATK for variant analysis, use hg_g1k_v37. (If you were using RNA-seq tools for expression analysis, I would recommend hg19, to take advantage of the iGenomes datasets). Best wishes for your project, Jen Galaxy team On 11/15/12 2:57 AM, David Sims wrote: Hi, Is it possible to use SNPeff with genomes other than worm. This seems to be the only option on the main Galaxy server. Thanks, David ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
Re: [galaxy-user] SNPEff - Reports Gain of Stop Codon as FRAME_SHIFT in some cases
Thanks John, Pablo, Updates are of course welcomed in the Tool Shed. Thanks for letting the Galaxy community aware that this may come up during analysis. Best, Jen Galaxy team On 12/13/11 12:17 PM, John David Osborne wrote: Hi Pablo, Correct me if I am wrong, but I believe that SNPEff doesn't check the inserted sequence when computing the effect of an insertion? For instance an insertion of TTTA will be reported as a frameshift mutation. In the majority of cases this is fine, however if the current reading frame from the ORF annotation is the negative strand and the correct frame is selected the new codon will be: TAA T… The TAA is actually a stop codon, so the real effect of this insert should be insertion of a STOP CODON, not a frame shift in this instance. This is minor I know, but I though to report and make people aware. I am using version 2.02 of SNPEff, but I don't see this fix reported up to 2.04. -John ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-user] SNPeff tool?
Hi, I've had a few email chats with the author of snpEff and the fly in the ointment from my perspective is getting the vcf files it needs through Galaxy. As I understand it there is no way currently of getting the BAM/SAM files into the right input format so snpEff can use it within a Galaxy setup. So, whatever you do you'll still need one or two command line steps. We have a copy of snpEff here at Bristol on our Galaxy and when we did that we then realised there was no Galaxy method (that we could think of) for getting the input file ready for snpEFF to use. This is a pity as its actually a very nice piece of software with a nice professional looking output. Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 13:55, Dannon Baker wrote: Hi Laura, While the SNPeff developers have made Galaxy wrappers available, this is not a tool we currently have installed for use on the Galaxy server at main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public Galaxy servers that offer this tool, but if you have access to a local or cloud galaxy server you could use the provided wrapper to install the tool for use there. Thanks! -Dannon On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote: Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-user] SNPeff tool?
I got it working just fine on my local server. Could you expand on your vcf issue? I generate the vcf using gatk. Sent from my iPhone On Nov 8, 2011, at 6:36 AM, David Matthews d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk wrote: Hi, I've had a few email chats with the author of snpEff and the fly in the ointment from my perspective is getting the vcf files it needs through Galaxy. As I understand it there is no way currently of getting the BAM/SAM files into the right input format so snpEff can use it within a Galaxy setup. So, whatever you do you'll still need one or two command line steps. We have a copy of snpEff here at Bristol on our Galaxy and when we did that we then realised there was no Galaxy method (that we could think of) for getting the input file ready for snpEFF to use. This is a pity as its actually a very nice piece of software with a nice professional looking output. Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 13:55, Dannon Baker wrote: Hi Laura, While the SNPeff developers have made Galaxy wrappers available, this is not a tool we currently have installed for use on the Galaxy server at main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public Galaxy servers that offer this tool, but if you have access to a local or cloud galaxy server you could use the provided wrapper to install the tool for use there. Thanks! -Dannon On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote: Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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/ ___ 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/
Re: [galaxy-user] SNPeff tool?
Hi, Yes, I see that you can generate the VCF files that way but there is no seamless way of doing it entirely from within galaxy - i.e. you need to come out of galaxy at some point (or am I missing something?). Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 14:39, Chorny, Ilya wrote: I got it working just fine on my local server. Could you expand on your vcf issue? I generate the vcf using gatk. Sent from my iPhone On Nov 8, 2011, at 6:36 AM, David Matthews d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk wrote: Hi, I've had a few email chats with the author of snpEff and the fly in the ointment from my perspective is getting the vcf files it needs through Galaxy. As I understand it there is no way currently of getting the BAM/SAM files into the right input format so snpEff can use it within a Galaxy setup. So, whatever you do you'll still need one or two command line steps. We have a copy of snpEff here at Bristol on our Galaxy and when we did that we then realised there was no Galaxy method (that we could think of) for getting the input file ready for snpEFF to use. This is a pity as its actually a very nice piece of software with a nice professional looking output. Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 13:55, Dannon Baker wrote: Hi Laura, While the SNPeff developers have made Galaxy wrappers available, this is not a tool we currently have installed for use on the Galaxy server at main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public Galaxy servers that offer this tool, but if you have access to a local or cloud galaxy server you could use the provided wrapper to install the tool for use there. Thanks! -Dannon On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote: Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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/ ___ 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
Re: [galaxy-user] SNPeff tool?
Gatk unified genotyper will take a bam/Sam and generate a vcf. Sent from my iPhone On Nov 8, 2011, at 6:54 AM, David Matthews d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk wrote: Hi, Yes, I see that you can generate the VCF files that way but there is no seamless way of doing it entirely from within galaxy - i.e. you need to come out of galaxy at some point (or am I missing something?). Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 14:39, Chorny, Ilya wrote: I got it working just fine on my local server. Could you expand on your vcf issue? I generate the vcf using gatk. Sent from my iPhone On Nov 8, 2011, at 6:36 AM, David Matthews d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk wrote: Hi, I've had a few email chats with the author of snpEff and the fly in the ointment from my perspective is getting the vcf files it needs through Galaxy. As I understand it there is no way currently of getting the BAM/SAM files into the right input format so snpEff can use it within a Galaxy setup. So, whatever you do you'll still need one or two command line steps. We have a copy of snpEff here at Bristol on our Galaxy and when we did that we then realised there was no Galaxy method (that we could think of) for getting the input file ready for snpEFF to use. This is a pity as its actually a very nice piece of software with a nice professional looking output. Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 13:55, Dannon Baker wrote: Hi Laura, While the SNPeff developers have made Galaxy wrappers available, this is not a tool we currently have installed for use on the Galaxy server at main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public Galaxy servers that offer this tool, but if you have access to a local or cloud galaxy server you could use the provided wrapper to install the tool for use there. Thanks! -Dannon On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote: Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.orghttp://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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.orghttp://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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.orghttp://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/ ___ The Galaxy User list should be used for the discussion of Galaxy
