...
- General introduction (SPHS)
- Getting started at TACC
- Linux refresher (SPHS)
- Using TACC's Lonestar Cluster
- Introduction to next-gen sequencing technologies presentation? (??)
- Application: Single-nucleotide variant (SNV) calling
- Workflow diagram of variant calling
- Evaluating your raw sequencing data (??)
- Introduction to mapping presentation (JB)
- Mapping tutorial (bowtie2, BWA) (JB/GC)
- Integrative Genomics Viewer (IGV) tutorial (JB)
- start diploid mapping
Enrichment modules (4:30-5:
...
30)
- Installing Linux virtual machine on Windows (DP)
- Sharing Linux tricks (SPHS)
...
- Introduction to variant calling (SAMtools) (SPHS - expand to diploid, cover GATK pipeline; annovar seqanswer)
- Visualize mapped data at UCSC genome browser
- Annotating variants (SPHS/DA)
- Download presentation on Advanced Genome Variant Calling Barrick_AdvancedGenomeVariantCalling_2012.pdf
Enrichment modules (4:30-5:
...
30)
- samtools tricks (DP)
- Installing Linux tools (JB)
- Shell Scripting (SPHS/AB)
...