Center for Health Bioinformatics Galaxy Tutorials
Resource:: CHB Harvard Exome-Seq Workshop Types:: Tutorial, Datasets Domains:: Exome-Seq Owners:: Shannan Ho Sui, Oliver Hofmann, Radhika Khetani, Winston Hide, Center for Health Bioinformatics at the Harvard School of Public Health Formats:: Web Pages
Date:: 2013/01

This is one of a set of online tutorials created (and maintained!) by Shannan Ho Sui, Oliver Hofmann, and Winston Hide in the Center for Health Bioinformatics at the Harvard School of Public Health.

Sections:

  1. Initial quality control
  2. Read trimming and filtering
  3. Alignment
  4. Exome-Seq QC
  5. Variant Calling and visual exploration
  6. Variant Annotation
  7. Variant prioritization

Needed Tools

Uses many "standard" tools that exist on most Galaxy servers, and

  • FastQC
  • One of the FASTQ quality filters
  • A short read mapper (e.g., Bwa or Bowtie)
  • SAMtools
  • GATK
  • IGV or Trackster
  • o8 Variant Visualizer (online)