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• VCF Combine, missing chromosomes?!
  Hello, The VCF file output from VCF Combine only has data up until Chromosome 3. I checked the v...
• Naive Variant Caller doesn't output variants wile mpileup does
  I am interested in calling Illumina errors. Therefore, I need to output variants with such a low ...
• 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 Annotation Regions using ANNOVAR Annotate VCF
  Hello, I'd like to use ANNOVAR Annotate VCF via Galaxy Web (Galaxy Version 0.2) to annotate vari...
• Running SnpEff on Galaxy
  Hello, I would like to annotate a .vcf file and also summarize possible effects variants can hav...
• Filtering Variants using Snpsift filter and SnpEff
  Hi, I have a bunch of variants in .VCF file which I got through the unified genotyper tool. Now ...
• ANNOVAR galaxy returning an empty file
  I am working through a project that requires me to Identify genes with polymorphic sites using AN...
• VCF output from Mpileup tool
  Hi everyboy, I am trying to call SNP using the SAM Tools → mpileup in Galaxy. Since the input ...
• Galaxy VCF Combine combines only to chr13
  Hello,  I am using Galaxy with vcflib (Garrison, Erik (2015). vcflib). I have two vcf files, whi...
• Followed Exome-Seq tutorial, but Gemini Load not working
  Hello! I am performing a study with data from 80 cancer patients, half of which showed one sympt...
• 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...
• Variant Recalibrator in Galaxy
  Hi, I am trying to run Variant recalibrator for SNPs and indels separately. Both the times I get ...
• Variant mapping workflow and tutorial in Galaxy
  Hi, I have a zebrafish mutant that I am trying to map. So I did the mapping crosses and sequenced...
• Filter Varscan VCF
  Hello, I have a VCF file obtained from the Varscan tool. I want to filter the variants based on ...
• bam to VCF
  Hi, I am trying to get all the variants from sequencing data. From fastaq, I got BAM files. Then...
• Slice VCF not retaining INFO data
  Hi folks   I'm using the Slice VCF tools to extract variants from a .vcf file that fall within ...
• Variant Annotation In Gatk Tools
  Hi all, I am analyzing some targeted resequencing data. I was trying to use Variant Annotation...
• Mpileup with vcf output?
  Hello, I noticed that the "mpileup" tool that gives an output file in vcf format is no longer av...
• 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...