Genome Variant Analysis Course 2014

• General introduction to Genome Variant Analysis (GVA14)

• Linux refresher and environment setup (SPHS)

  • Step 1: Connecting to and establishing a profile on Lonestar (GVA14)

  • Step 2: Editing files

  • Step 3: Final explanations

  • Linux/Unix command cheat-sheet: 

• Using TACC's Lonestar Cluster (SPHS)

  • Diagram of Lonestar's directories

  • Lonestar tips & tricks cheat-sheet: 

  • Diagram of running a job on Lonestar

  • launcher-creator.py cheat sheet: 

  • Submitting a simple job using launcher_creator.py

• Additional Useful Links (GVA14)

• Handout: 

• Presentation: 

• Tutorial: Mapping tutorial (bowtie2, bwa) (GVA14)

• Tutorial: Integrative Genomics Viewer (IGV) (GVA14)

• Bonus: Evaluating and processing raw sequencing data (GVA14) 

• Bonus: Mapped read data evaluation (samstat, SAMtools) (GVA14)

Part 1. Single-nucleotide variants (JB)

• Presentation: 

• Tutorial: SNV calling tutorial (SAMtools) (GVA14)

• Presentation: 

• Tutorial: SV calling tutorial (SVDetect) (GVA14)

• Tutorial: Advanced variant calling tutorial (breseq) (GVA14)
  

• Overview: whole genome and complexity reduction methods (GVA14)

  • Human Trios

  • An introduction to GATK

  • Exomes: capture & metrics

  • Tumor/normal analysis with Virmid (GVA14)

• Samtools mpileup in more detail (optional) 

• Annotating variants with annovar (GVA14)

• Filtering & screening variants

• Evaluating performance

• The importance of validation (discussion)

Day 4: Rare Variant Detection in Populations

Part 1. Sequencing of mixed populations

• Presentation: Sources of errors, and computational methods to improve detection.

• Tutorial: Breseq Identification of Variants in Mixed Population Sequencing (GVA14)

• Tutorial: Comparison of mixed population sequencing options (GVA14)

Part 2. Targeted Sequencing of Molecular Indexed Libraries. 

• Presentation: Alternative Library Preparation Methods 

• Presentation: Experimental design

• Tutorial: SSCS Read Generation

• Tutorial: Breseq identification of rare variants within targeted regions

• Discussion: Full results of SSCS sequencing, and use of autocorrelation

Resources

• NGS Course Resources Tool List

• GSAF adaptor and barcode sequence resource

• Working on TACC from your Mac or PC

  • Editing files, more detail

• Scott's list of linux one-liners

• Installing Virtual machine & Linux on Windows

• Example BWA alignment script

• Variant calling with GATK (SPHS)

• Visualize mapped data at UCSC genome browser (AB)

• Genome variation in mixed samples (FreeBayes, deepSNV) (JB)

• SRA toolkit and Exercises (AB)

• Shell Scripting (SPHS/AB)

• Installing Linux tools (JB)

• Custom Genome Databases

• Evaluating & Visualizing assemblies (bacterial, SPHS) 

• Genome Assembly Examples (SPHS) 

• Tutorial: Genome Assembly (velvet) (SPHS)

• Visualize mapped data at UCSC genome browser (AB)

• ddRAD (Stacks tutorial: http://evomics.org/wp-content/uploads/2013/03/cesky_2014_RAD_tutorial_updated.pdf) , Tn-Seq?