Re: [galaxy-user] Question about Unified genotyper
Hello Mathew, Carlos is correct the the tools in the group "NGS: GATK Tools (beta)" will require that the data is mapped/associated with the reference genome "hg_g1k_v37". Belinda has offered to help with the details that go beyond Galaxy and that is great - the GATK forum is definitely the best resource for questions specific to that tools set once you know that the basic Galaxy datasets are correct. Freebayes, on the other, will work with "hg19". Other users have perform an independent mapping run to avoid complex data manipulations/sorting. Please feel free to send in a bug report if problems persist. When submitted a bug report, send from the error dataset (just one is enough if all of the problems are in the same history) and put in the notes all of your concerns. Be sure to include this email address in the comments if your Galaxy account uses a different one. Also be sure to leave all input and error datasets that you would like feedback about in an undeleted state in your history. Undelete if necessary. Thanks! Jen Galaxy team On 8/6/12 7:30 AM, Mathew Bunj wrote: I have been trying to use either Unified genotyper or Freebayes on one of the Bam file. Both are failing. 1. With Unified genotyper it give me message saying Sequences are not currently available for specified build. I have hg19 related data and using default settings (pick up hg_g1k_v37 no other option). I am not sure why it is giving me this error. 2. As an alternative I tried to run Freebayes with default setting and choosing hg19 - it i snot giving any specific message but undetr bug icon gives me -killed. Now in order to make sure my Bam is OK, I tested out side Galaxy mPile up and with in Galaxy pile up. Any suggestion why UNified genotyper is not working. If needed I can share my history. Thanks. ___ 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] Question about Unified genotyper
Hi Mathew, If you are new to the GATK tools you may want to read some of our introductory materials at this link: http://www.broadinstitute.org/gatk/guide/topic?name=intro You will find some documents explaining what input files you can use, what are the constraints, and plenty of information about using tools like the Unified Genotyper in the GATK Guide. If you have questions that are specific to the GATK tools, feel free to ask them in our forum and we will do our best to help you. http://gatk.vanillaforums.com/ Good luck! On Tue, Aug 7, 2012 at 2:01 PM, Carlos Borroto wrote: > Hi Mathew, > > Regarding 1 you might want to read this thread: > > http://user.list.galaxyproject.org/Problem-with-Depth-of-Coverage-on-BAM-files-GATK-tools-td4654147.html > > All tools from GATK are limited to hg_g1k_v37 as far as I know. > > Best, > Carlos > > On Mon, Aug 6, 2012 at 10:30 AM, Mathew Bunj wrote: > > I have been trying to use either Unified genotyper or Freebayes on one of > > the Bam file. Both are failing. > > > > 1. With Unified genotyper it give me message saying Sequences are not > > currently available for specified build. I have hg19 related data and > using > > default settings (pick up hg_g1k_v37 no other option). I am not sure > why > > it is giving me this error. > > 2. As an alternative I tried to run Freebayes with default setting and > > choosing hg19 - it i snot giving any specific message but undetr bug icon > > gives me -killed. > > > > Now in order to make sure my Bam is OK, I tested out side Galaxy mPile up > > and with in Galaxy pile up. Any suggestion why UNified genotyper is not > > working. If needed I can share my history. > > > > Thanks. > > > > > > > > > > ___ > > 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] Question about Unified genotyper
Hi Mathew, Regarding 1 you might want to read this thread: http://user.list.galaxyproject.org/Problem-with-Depth-of-Coverage-on-BAM-files-GATK-tools-td4654147.html All tools from GATK are limited to hg_g1k_v37 as far as I know. Best, Carlos On Mon, Aug 6, 2012 at 10:30 AM, Mathew Bunj wrote: > I have been trying to use either Unified genotyper or Freebayes on one of > the Bam file. Both are failing. > > 1. With Unified genotyper it give me message saying Sequences are not > currently available for specified build. I have hg19 related data and using > default settings (pick up hg_g1k_v37 no other option). I am not sure why > it is giving me this error. > 2. As an alternative I tried to run Freebayes with default setting and > choosing hg19 - it i snot giving any specific message but undetr bug icon > gives me -killed. > > Now in order to make sure my Bam is OK, I tested out side Galaxy mPile up > and with in Galaxy pile up. Any suggestion why UNified genotyper is not > working. If needed I can share my history. > > Thanks. > > > > > ___ > 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/
