[galaxy-user] Question about Unified genotyper

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

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: >

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 abo

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 b