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• To varscan mpileup data
  HI, I have run the mpileup (process is completed and successful), and was trying to analyse the p...
• VarScan on Galaxy
  Hi All ive been trying to use varsacn on my pileup file in Galaxy  in the results, i get "N" in...
• difference between MPileup multi-way pileup of variants and Generate pileup from BAM dataset
  hello everobody , in my project , i have to detect the variants (SNP and indels) in my genome se...
• Varscan and pileup files
  Hi, I would like to perform a variant calling analysis using Varscan and I used Generate pileup ...
• How do I process multiple pileup files at once with Varscan to get the vcf files?
  I have a list of 100 SRA IDs for which I need to get the VCF files using VARSCAN. VARSCAN takes...
• This job was terminated because it used more memory than it was allocated (new post)
  To Galaxy, I've read on this forum about the proposed solutions to this memory issue. Other than...
• Getting an excel list of variations from Varscan or FreeBayes .vcf files
  I have whole genome sequence from Saccharomyces cerevisiae strains and I'm looking for their vari...
• Varscan unable to compare somatic with germline samples
  Hi, I am trying to compare tumour with normal to call variants in varscan. I dont seem able to d...
• annotation issues with ANNOVAR
  Hi All, I am trying to annotate a Vcf file that I generated using the VarScan. I could visualize...
• 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...
• Too few reads after VarScan on RNA-Seq data?
  Hi all, I have been trying to initiate a protocol to call SNPs in RNA-Seq data, but have had a f...
• snp detection for sra files
  hello i need an urgent help i want to detect snp for sra files i did bwa and convert the file i...
• Filtering using BED file
  I have generated mpileups and I wish to filter the desired variants using a BED file. I have done...
• How to filter SNP and Indel data
  I have mapped my sequence with a wild type sequence using Bowtie2 and obtained around 8000 SNPs a...
• Need help with "Varscan" tool
  In my browser window, Varscan for variant detection does not allow me to add datasets. What is wr...
• Varscan QUAL field
  Hi, I am running Varscan through the galaxy interface. Although the tool runs correctly and gen...
• Varscan on multiple samples generates error
  Hello, I am using "samtools mpileup" to generate a pileup file from my .bam dataset and then pas...
• intron retention analysis
  Hi! I am hoping to use the analysis tools that are available in Galaxy to achieve my tasks. I am ...
• galaxy full details
  describe about fastqc,fastq groomer, bwa ilumima, sam tools, mpileup, varscan, vcf filter, plz te...