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- Introduction to variant calling (SAMtools) (SPHS - expand to diploid, cover GATK pipeline; annovar seqanswer)
- Assess Visualize mapped data (VCF? BAM?) at UCSC genome browser (AW)
- Annotating variants (SPHS/DA)
- Download presentation on Advanced Genome Variant Calling Barrick_AdvancedGenomeVariantCalling_2012.pdf
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- samtools tricks (DP)
- Installing Linux tools (JB/)
- Shell Scripting (SPHS/AB)
Extras
- SRA toolkit, more 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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