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• Suggestions for variant callers/ problem with BCF view
  Samtools mpileup only outputs genotypes fields for samples when a BCF output is selected. The BCF...
• Spliting a VCF for some genotypes
  Dear All I have a VCF file of 250 genotypes developed using HaplotypeCaller at GATK tools. now I ...
• How to combine genotypes into one VCF file?
  Hi, I have tried using VCF combine to merge 3 files from 3 different individuals into a single VC...
• Need help with "Unified Genotyper" tool
  Every time I try to use the Unified Genotyper Tool under GATK, I receive the following error mess...
• Counting Rna-Seq Reads Per Class.
  Hi All, I have been trying to count the number of RNA-seq reads that fall into the various Cuffli...
• Paired collection option in Unicycler
  I did sequencing twice for one isolate. So, I have two data datasets (four fastq files). I am won...
• Need help with "Unified Genotyper" tool
  Hi there, I would like to add the file 'dbsnp_137.hg19.vcf' to my GATK unified-genotyper analysi...
• Question About Unified Genotyper
  I have been trying to use either Unified genotyper or Freebayes on one of the Bam file. Both are ...
• How To Use Gatk Unified Genotyper With "A List Of Genomic Intervals Over Which To Operate" Option
  Hi, I would like to run "Unified Genotyper" on a region of a BAM file, I see the advance option ...
• Unified Genotyper in GATK issue
  Hi, I have executed Unified Genotyper in gatk in galaxy wiki and I have got the following error:...
• 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...
• Exome Sequence Analysis Question - using GATK Unified Genotyper
  Hi everyone, I'm tring to call SNVs and short Indels using the GATK Unified Genotyper. I have pr...
• Unified Genotyper problem
  I am trying GATKTool "unified genotyper" for variant calling but i am facing error. Is this tool...
• Faire-seq peak calling
  Hello, I have question related to Faire-seq peak calling. Since I am not a Linux user, I have onl...
• Unable to convert FASTAQ file into NCBI standered FASTA file format
  Hi I wanted align multiple alignment of several Salmonella Typhi isolates in bioedit software. I ...
• False negative results in GATK unified genotyper output
  Hi all, I'm having some problems with the output of the GATK unified genotyper.  Essentially I ...
• How to compare two libraries
  Dear Service, I load in Galaxy server about 10 histories. Each one is composed of a fastq file a...
• Genotype Concordance - bcftools - stats?
  I've been trying to find a tool in galaxy that works for calculating genotype concordance between...
• HELP! A Runtime Error in Running Unified Genotyper
  Hi, I'm having problems in running the workflow of cloudmap. When it gets to "Unified Genotyper...
• Import Data In Rgenetics
  dear Galaxy users, I would like to import genotyping data in Rgenetics and I can't succeed. I hav...
• renaming datasets in workflows, small probelm with Unified Genotyper and output_vcf
  Hi  I have been successfully following the renaming datasets in workflows advice , it is very ve...