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• bcftools view will not read VCF file
  Hi, BCFtools view allows the reversible conversion between BCF and VCF formats. In Galaxy the de...
• Galaxy custom tool doesn't exit from "waiting to run" condition
  I have some trouble with custom tool on my local Galaxy. I have a script that exactly works. It h...
• BCFtools output tabular
  Hi, I'm sorry for my naive question (but this is my first analysis)... Analysis: 19 PCR targett...
• Mpileup with vcf output?
  Hello, I noticed that the "mpileup" tool that gives an output file in vcf format is no longer av...
• Samtools Output
  Hello, I am having trouble replicating the great output you get after running samtools "Filter p...
• Bcf To Vcf
  I wasw wondering if there is any option in Glaxy to convert bcf format to vcf format? Thanks Ka...
• Need help with "ANNOVAR Annotate VCF" tool
  Hi!  I entered a vcf file into the annovar tool.  It looks like it ran and tells me then number o...
• What is causing this MPileup error in Galaxy?
  Hello, I'm new to galaxy and next gen sequencing.  I'm trying to generate a VCF file from whole ...
• Reads are 0 in htseq-count
  Hello, I have a trouble using htseq-count, I used TopHat to aling my data, but when I tried to c...
• Need help with "VCF-VCFintersect:" tool
      Tool name: VCF-VCFintersect: Tool version: 0.0.2 Tool ID: toolshed.g2.bx.psu.edu/repos/ant...
• Using a JSON object for visualization plugin
  I need a JSON file to be recognized by a visualization plugin named - 'igv'. By following the Vis...
• mpileup warning and problem with bcftools call
  I am using mpileup and bcftools call in Galaxy. Mpileup produces a VCF output file, but also give...
• is the VCF filtering function working?
  Hi there, I was wondering if the NGS: VCF manipulation: VCFfilter function is actually working. ...
• Parallelism with Multiple Outputs : HOW?
  First Question, Where in the Galaxy file system are the parallelism modules defined? I.e. where ...