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• Workflow reference genome
  Dear GALAXY team, In a workflow, is it possible to change the database type of an output file fr...
• obtaining SNP/SNVs from vcf or BAM files with galaxy?
  Hi there! I am working on a project identifying SNPs/SNVs of a few sequences and was wondering i...
• How to combine genotypes into one VCF file?
  Hi, I have tried using VCF combine to merge 3 files from 3 different individuals into a single VC...
• Determining Genotype/Phylogeny in Galaxy
  Hi, I am trying to determine the phylogeny/genotype of a series of sequential clinical Aspergill...
• Need help with "Unified Genotyper" tool
  Hi there, I would like to add the file 'dbsnp_137.hg19.vcf' to my GATK unified-genotyper analysi...
• How to intersect vcf files for commonly mutated genes only (not the exact mutation)
  Hi all, I intersected two vcf files using vcf-vcf intersect on usegalaxy.org and I realized that...
• variants intersect with dbSNP
  Hello, I have a VCF file and I would like only keep variants which are in dbsnp_135.hg19.vcf. H...
• Mpileup with vcf output?
  Hello, I noticed that the "mpileup" tool that gives an output file in vcf format is no longer av...
• VariantsToTable? Extract AF from INFO column of VCF
  Hi all, I would like to extract the AF from the INFO column of GATK Unified Genotyper VCF files (...
• galaxy doesn't recognise dbSNP file I uploaded
  Hi I'm somewhat new to the game and struggling with the GATK unified genotyper. I found a dbsnp...
• Exome Sequence Analysis Question - using GATK Unified Genotyper
  Hi everyone, I'm tring to call SNVs and short Indels using the GATK Unified Genotyper. I have pr...
• Variation in coding region
  Dear I filtered five VCF files by using GATK tools with option "Select Variants from VCF File" a...
• Dealing with rows in tabular data
  Hello Experts I am using use galaxy for genome wide SNP discovery. I have discovered about 770,0...
• Question About Unified Genotyper
  I have been trying to use either Unified genotyper or Freebayes on one of the Bam file. Both are ...
• Loss of original VCF file; therefore in Galaxy, can I use VCF manipulation on an excel file (originally converted from VCF format)
  I have inherited a project where the original VCF files were lost. I have the excel files derived...
• Filtering A Vcf File
  I’m using a local instance of Galaxy. I’d like to filter a VCF file for SNPs that have passed fi...
• Split VCF file
  I would like help splitting a large vcf file containing WGS data into smaller files. Using Gala...