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• Freebayes variant recalibration and quality filters
  I am working on freeBayes pipeline for variant calling on BRCA sequence aligned with BWA and I ha...
• Problem with indels not appearing in FreeBayes output
  Hello, I have 6 datasets for 3 individuals (forward and reverse DNA seuqences) that I am trying ...
• FreeBayes database/build database?
  What if I cannot find my reference sequence in the database/Build option when I want to check the...
• Loading VCF into a local IGV fails with metadata error during data prep step
  Although my genome sequence is part of the list of options thanks to custom build, the link to di...
• 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...
• Use galaxy error segmentation fault Freebayes filter
  Hello, I am running out of memory, even though I deleted some of the work.
• Trying to understand the steps for 'identify DNA polymorphism sites'
  Greetings! My partners and I got this homework. We're not specialized in bioinformatics or anythi...
• (No Subject)
  Hi, Can't seem to find an answer to this on your wiki site and it's not in the tutorial. I wo...
• Mpile up output
  Hi  I am using Mpileup using SAM tools version 1.2+htslib-1.2.1 to generate variants. The tool w...
• empty QUAL field
  Hi, I'm trying to analyze polymorphic sites in the individual. After running Naive Variant Calle...
• How do I determine the correct filtering threshold in VCFfilter after running FreeBayes
  I would like to perform a VCFfilter on my FreeBayes data but I'm not sure how to choose the corre...
• long running time on freebayes with a bam file
  Hi, I am using Galaxy freebayes to call variants on a WES bam file. It apparently takes very long...
• Snp Calling Problems
  Dear all, I have been looking for an answer to my problem in all the Galaxy Support resources bu...
• Freebayes coverage enquiry
  Silly question time: I have been using Freebayes to find variants in my data, using the simple s...
• Variant analysis help
  Hello, I am trying to identify variants using data from a BAM file generated from an RNA-Seq exp...