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- General introduction (SPHS)
- Getting started at TACC
- Introduction to mapping
- Evaluating your raw sequencing data
- Alignment with bowtie, BWA (JB/GC)
- Download Presentation on Mappers, etc.|^NGS NGS+class 22Mar12.ppt|||||||||||||||||||\
- Using the Integrative Genomics Viewer (IGV) (JB)
- Workflow diagram of variant calling
- start diploid mapping
Enrichment modules (4:30-5:00)
- Installing virtual machines OR samtools tricks OR data formats for UCSC genome browser Linux virtual machine on Windows (DP)
- Sharing Linux tutorial tricks (SPHS)
Extras
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- Introduction to variant calling (SAMtools) (SPHS - expand to diploid, cover GATK pipeline; annovar seqanswer)
- Assess mapped data (VCF? BAM?) at UCSC genome browser (AW)
- Annotating variants (SPHS/DA)
- Download presentation on Advanced Genome Variant Calling|^Barrick_AdvancedGenomeVariantCalling_2012.pdf|||||||||||||||||||||\
Enrichment
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modules (4:30-5:00)
- samtools tricks (DP)
- Installing Linux tools (JB/)
- Shell Scripting (SPHS/AB)Maybe start tophat via script (DA)
Extras
- SRA toolkit, UCSC Genome Browser
- Mapped read data evaluation (SAMtools) (SPHS)
- Calling variants in diploid genomes
- Variant calling with GATK
- Genome variation in mixed samples (FreeBayes, deepSNV)
- Identifying structural variants (SVDetect)
- Practical advice - short read re-sequencing data
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Enrichment module (4:30-5:30)
- Maybe show how to run tophat here instead of end of day 2?Start tophat via script (DA)
Extras
...