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• GATK tools and reference genomes
  The GATK tools are present as a beta version, and I tried to use selection or filtration, and the...
• BAM header using BWA-MEM in galaxy compared with GATK resource bundle (hg38) - deprecated tools in Galaxy
  Hi! I am trying to perform some analysis using GATK in order to identify mutations. Long sotry s...
• Adding reference genome to Galaxy
  Hi, I want to add reference genome(hg19) from UCSC main table to my Galaxy account,how can I do t...
• Galaxy workflow RealignerTargetCreator reference genome not available
  I am (still) trying to implement the GATK best practises pipeline using Galaxy workflows. I manag...
• Realigner Target Creator (GATK) with a custom or native local genome
  Hi! I cannot introduce any local reference genome in the Realigner Target Creator. Is this becau...
• Problem with Refreence Genome in Gatk Tools
  Hi, I am attempting to run a variant call on Gatk. I used the "Validate Variants" tab first, how...
• GATK Select Variants Reference Genome
  Hi, I'm trying to use GATK Tools Select Variants on VCF files of whole genome sequencing data, ...
• Need to use hg38 as reference in GATK
  I need to use the SNP calling tool in GATK, but I can only find hg37 as the reference under the G...
• GATK indel realigner using custom reference
  I've been using some SAM (converted to BAM) files and some partial genome assemblies (custom refe...
• 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
  Dear happy users of Galaxy, We are running Galaxy locally. It's a very fine tool! By now everyt...
• DBSNP, Variant Caller
  I have a VCF file from FreeBayes Variant caller. However I want VCF file to have dbSNP (rsID). T...
• GATK 2.8 reference genome and "data_manager_gatk_picard_index_builder"
  Hi everyone, Now that I succeeded on installing GATK2.8, and I am trying to use it. According to...
• What to write in "Using reference genome" and "Annotation Regions"sections ?
  Hey, I am trying to use GATK through Galaxy and trying to call variants from my vcf file. "Selec...
• Problem With Gatk Tools Not Accepting Bam File As Input
  I am using GATK tools on the useGalaxy main server to detect variants in a mutant C. elegans whol...