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  I've been using some SAM (converted to BAM) files and some partial genome assemblies (custom refe...
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  My workflow paused due to an error at the Realigner Target Creator (GATK intervals) step. An err...
• Need help with "Realigner Target Creator" tool
  Hi every one, If somebody familiar with using the GATK realigner target creator on galaxy? My d...
• "Realigner Target Creator" tool on usegalaxy.org Locally cached reference unavailable
  HI  I have a bam file generated using a cached reference  (not a user custom one).  However if I...
• issue with realigner target creator
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• Realigner Target Creator will not run?
  I have been running the pipeline below to try and call SNPs from RNA-Seq data but have encountere...
• Question About The Gatk Tools
  Hi, I just uploaded the BAM file for an exome sequencing sample and was trying to use the GATK t...
• Gatk - Base Recalibrator
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• Where to get SNPs and Indels?
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• Problem with RealignerTargetCreator in the CloudMap workflow
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• installation toolshed errors - realigner target creator
  Hi,  I installed galaxy on Ubuntu and I try to keep it as simple as possible so do not use any o...
• Gatk Error Argument With Name 'T' Isn'T Defined
  Aloha. I am using GATK in Galaxy for the first time, on a local Galaxy server, and when I try to ...
• suite_samtools_1_2 EOF marker absent error
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• Reference genome: no options available - use Custom reference genome
  Hi, I am using galaxy and in particular a modified version of a workflow that I found on usegala...
• GATK 2.8 Realigner Target Creator reference genome issue
  Hello everyone, I want to use Realigner Target Creator provided in the toolshed with the GATK ve...
• Realigner Target Creator Error
  Hi, I keep running into this problem and can't seem to figure out how to solve it... I'm using ...
• Error running Realigner Target Creator on Cloudman
  Hi, While running the tool "Realigner Target Creator" on cloudman I encounter the following erro...
• Identification of SNPs
  I was trying to realign my bam files through GATK realigner target creator, so this error occurre...
• Help with GATK protocol
  I wish to call variant using the GATK workflow. However, I am having problems 1. Indel re-aligne...
• failure preparing job - workflow
  Hi,  I managed to setup my own server (running on Ubuntu) and managed to perform the necessary a...
• RealignerTarget Creator in Galaxy
  Hi, I am just starting to use galaxy. I am having a trouble using the GATK tool called Realigner...
• Error with "Realigner Target Creater" on Galaxy
  I used Realigner Target Creater on Galaxy with GATK --> ucsc.hg19.fasta and Mills and 1000G go...