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• 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...
• Suggestions for variant callers/ problem with BCF view
  Samtools mpileup only outputs genotypes fields for samples when a BCF output is selected. The BCF...
• 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...
• 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 ...
• Trouble renaming the dataset output from Naive Variant Caller in Workflow
  Hi I am having trouble renaming the Dataset outputs from 'Naive Variant Caller' in the Galaxy wo...
• empty QUAL field
  Hi, I'm trying to analyze polymorphic sites in the individual. After running Naive Variant Calle...
• bam to VCF
  Hi, I am trying to get all the variants from sequencing data. From fastaq, I got BAM files. Then...
• 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...
• help with the acount of the total number of variants fron vcf file
  i have a vcf file and now how can i proceed to have the number ofsingle nucleotide variants, the ...
• 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...
• VCF file samples not called
  I'm trying to identify polymorphisms in three samples. When I get the VCF file there are many var...
• Variant Recalibrator in Galaxy
  Hi, I am trying to run Variant recalibrator for SNPs and indels separately. Both the times I get ...
• 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...
• GATK and c. elegans
  Hey, Has anyone ran *C. elegans* data through GATK? I have the dbsnp file but am stuck on the V...
• 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...
• True variant not called by Varscan
  Hi, I'm using the Varscan tool to call SNPs and INDELs. There are some TRUE variants that are no...
• 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...
• Local Galaxy Biolinux naive variant caller installation
  I'm trying to install Naive Variant Caller on the local Galaxy server that came pre-installed wit...
• VCF filter filters everything; best forum for questions
  I have datasets that have been generated by the naive variant caller, and wish to filter them for...
• 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 ...
• RefSeq Annotation using SnpEff
  Hello, I am working with human whole genome sequence. I have called variant using samtools and I...