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• 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 ...
• RefSeq Annotation using SnpEff
  Hello, I am working with human whole genome sequence. I have called variant using samtools and I...
• What Galaxy tools can preprocess VCF file before running the SNPEff annotation process?
  What Galaxy tools can preprocess VCF file before running the SNPEff annotation process? We have t...
• Need help with "SnpEff" tool
  hi i am trying to use snpeff on galaxy...i give vcf file but i dnt know in genome portion what i ...
• Running SnpEff on Galaxy
  Hello, I would like to annotate a .vcf file and also summarize possible effects variants can hav...
• using snpEff via galaxy
  ı have A question about Annotating variants with SnpEff following this tutorial (https://galaxypr...
• How to annotate 500 vcf files using SNPEff or smth else and put every separate result in a folder with the name of the SRA identifier?
  How to annotate 500 vcf files using SNPEff or smth else and put every separate result in a folder...
• Filtering for the frequency of ALT alleles
  Hi, When running CloudMap unmapped mutant workflow, I get a SnpEff file with Homozygous or heter...
• Variant Annotation In Galaxy
  Hallo Galaxy users, I would like to annotate variants (in vcf file) found in my bacterial genome...
• Add RefSeq ID to VCF file
  Hello! I am working with whole genome sequence of homo sapiens. I aligned my sample data with hg3...
• snpEff tool not available
  Hi guys,   I'm trying to use the snpEff tool and both the CloudMap: Check snpEff Candidates and...
• Need help with "SnpEff" tool
  Hi there, I'm trying to run SnpEff on Galaxy, but the only Genome that it gives me access to is ...
• Filter Tool
  (Starting new thread on galaxy-user.) Jagat, It depends what filter tool you're using and what ...
• SNPeff for date palm
  Now I get the  .VCF  file  from  Samtools  and   i want  to  annotate  My SNPs. i have choose to ...
• Cuffdiff Without Gene Annotation
  Hello guys, I went through the RNAseq workflow (I didn't do Cuffmerge) and from the Cuffdiff outp...
• snpsift filter fatal error
  Hi all, I want to use SnpSift Filter, but each time an error occurred. any idea? thanks in advanc...
• Zygosity of mutations
  Hi all, While performing an analysis of NGS data I am not getting the column for mutation zygosit...
• SnpEff (Galaxy) troubleshoot
  I have got Mpileup data. I wish to further understand SNP effect using snpeff. Unfortunately, in ...
• Locally cached annotation not available for featureCounts
  Hi all, For my RNAseq analysis, I am using the featureCounts tool to measure gene expression fr...