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- Evaluating your raw sequencing data (JBDP/AB)
- Mapped read data evaluation (SAMtools) (SPHS, DP/AB)
- Practical advice - Final odss odds & ends for short read re-sequencing data
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- Example genome variant calling pipeline (JBSPHS)
- Variant calling workflow diagram:
- Variant calling workflow diagram:
- Introduction to genome variation
- (JBSPHS)
- Variant calling tutorial (SAMtools) (JBSPHS)Variant calling with GATK
- Calling variants in diploid genomes (SPHS)
Enrichment module (12:30-1:30)
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Extras
- Calling variants in diploid genomes Variant calling with GATK (SPHS)
- Annotating variants (SPHS)
- (JB)
- Visualize mapped data at UCSC genome browser (AB)
- Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
- Identifying structural variants (SVDetect) (JB)
- SRA toolkit (AB)
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