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• FASTQ to viewer to variant calling
  Hello, I am new bioinformatics and am trying to teach myself how to do some basics. I have FAST...
• Correct way of merging samples for father, mother, child trio variant calling
  I am new to NGS data analysis and I'm working in a multiple-sample variant calling workflow. I ha...
• Variant analysis using Galaxy - tutorials, example workflows
  I have my FASTQ files, and I am trying to align them to the mouse reference genome, and perform v...
• VCF output from Mpileup tool
  Hi everyboy, I am trying to call SNP using the SAM Tools → mpileup in Galaxy. Since the input ...
• Freebayes variant recalibration and quality filters
  I am working on freeBayes pipeline for variant calling on BRCA sequence aligned with BWA and I ha...
• Whole Exome Sequencing
  I recently got on a project that is attempting to find novel mutations in certain diseases by com...
• Mark Duplicate Reads Error- "Value was put into PairInfoMap more than once"
  Hi everyone, I am relatively new to galaxy and have been trying to set up a workflow for variant...
• Problem with Refreence Genome in Gatk Tools
  Hi, I am attempting to run a variant call on Gatk. I used the "Validate Variants" tab first, how...
• 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...
• Does Galaxy NGS tools support targeted sequencing analysis?
  Glad to see Galaxy now provides support to do EXOME-seq analysis from FASTQ to Variant calling. K...
• Workflow to clean data prior to variant call
  Hi,  I would like some advice on the workflow I'm using. 1- I have WGS data from bacteria, I've...
• error in running MiModD Variant Calling
  I am a new user of MiModD (Previously, I use CloudMap to analysis WGS data from Hawaiian Variant ...
• Suggestions for variant callers/ problem with BCF view
  Samtools mpileup only outputs genotypes fields for samples when a BCF output is selected. The BCF...
• Mapping paired reads to reference genome, variant calling
  I am trying to map a trio of paired-end Illumina reads to a reference genome, then identify polym...
• BWA - History does not include a dataset of the required format
  Hello, I tried to aligned paired end reads with BWA (Map with BWA (version 0.2.3)) on my own Gala...
• BAM to VCF format
  I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads Q...
• Annovar is returning a file with only headers
  Hi I am trying to do some variant analysis. I have mapped the reads using hg19 as reference thr...
• GWAS: Fastq to BAM to VCF
  I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads Q...
• Depth of Coverage
  I am noticing that DP of those sites that will become eventually later variant calls are very muc...
• Commandline Bowtie2 and variant call help.
  Hello there! When you run bowtie2 to align the reads to the genome, some stats about the file ar...
• How to extract SNPs from galaxy workflow
  I exactly followed the below galaxy workflow that contain targetted re-sequencing data for a fath...
• Error in MiModD variant caling
  Hi I am using MiModD on galaxy to do mapping-by-sequencing. I used bowtie2 to do the alignments ...