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Day 1: Linux/TACC Introduction and Read Mapping
- Linux refresher
- Using TACC's Lonestar cluster (GVA14)
- Introduction to mapping (bowtie, BWA)
- Introduction to variant calling (SAMtools)
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- Variant calling with GATK
- Genome variation in mixed samples (FreeBayes, deepSNV)
- Identifying structural variants (SVDetect)
Even More Extras
- Download presentation on Advanced Genome Variant Calling|^Barrick_AdvancedGenomeVariantCalling_2012.pdf\
- Practical advice - short read re-sequencing data
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