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• Converting a CLC variant pipeline to Galaxy
  Hello, I have a recieved a VCF file wich was generated by CLC. Currently, I try convert the below...
• Help To Identify Variants With Clinical/Phenotype Associations
  Hi all, I have a dataset with potential pathological variants and I'd like to combine them to a ...
• ANNOVAR annotate cuts short the VCF file ?
  I uploaded a standard VCF that contains 57651 lines (or 57471 lines variant data) and ran it with...
• Help: Determining The Exon Number Of Exonic Variants
  Hi everyone, I have a list of genomic coodinates corresponding to exonic variants, and I'd like ...
• Whole Exome Sequencing
  I recently got on a project that is attempting to find novel mutations in certain diseases by com...
• Help Needed
  Hello, I have a list of variants(SNPs) that differ from reference sequence (in my human subject D...
• 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...
• SnpEff variant annotation
  Hello! I am trying to annotate variants (Human genome) by SnpEff annotate variants (Galaxy Versi...
• getting number of SNPs, insertion/deletion from VCF with VCFfilter
  Hello, I am trying to extract from a VCF file the number of SNPs: Single nucleotide variants , I...
• Suggestions for variant callers/ problem with BCF view
  Samtools mpileup only outputs genotypes fields for samples when a BCF output is selected. The BCF...
• Variant analysis using Galaxy - tutorials, example workflows
  I have my FASTQ files, and I am trying to align them to the mouse reference genome, and perform v...
• How to classify the variants into different groups?
  Hello, This is my first time using galaxy. I ran Free Bayes to detect the variants of a data set ...
• How to separate SNPs from other variant types in Galaxy?
  I have a VCF file with all the called variants. I want to keep just the SNPs. This is achievable ...
• DBSNP, Variant Caller
  I have a VCF file from FreeBayes Variant caller. However I want VCF file to have dbSNP (rsID). T...
• error using variant recalibrator in galaxy
      Tool name: Variant Recalibrator Tool version: 0.0.4 Tool ID: toolshed.g2.bx.psu.edu/repos/...
• Are there Structural Variant Analysis Software in Galaxy?
  Hello Galaxy, Do you know which software available on Galaxy is capable of performing structural...
• Chip-Seq, Encode Peaks And Galaxy
  Hi everyone, I have a list of genomic regions with some variants and would like to study the cor...
• How to extract SNPs from galaxy workflow
  I exactly followed the below galaxy workflow that contain targetted re-sequencing data for a fath...
• Problem with cloudmap workflow
  Hi I am using cloudmap workflow on Galaxy main sever to identify the mutation of mutant C. elega...
• empty QUAL filed in Naive Variant caller vcf output
  Hi, The QUAL field in vcf output of Naive Variant Caller is empty for all the variants. Any reas...
• finding gene locations and known SNPs for a list of genes
  I have a list of genes for which I need to find their respective location on the chromosome and a...