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 <mathewb...@yahoo.com> 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/
