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- Mapped read data evaluation (SAMtools)
- Installing Linux tools
- Integrated pipeline for microbial genome re-sequencing analysis (breseq)
- Calling variants in mixed populations
- Practical advice about some things to watch out for with short read re-sequencing data
- Calling variants in diploid genomes
- UCSC genome browser, SRA data downloads - 30 min - Anna
- Variant calling with GATK (use their wiki), more detail on .vcf format, look at Human data 1000 genome VCF files and describe how to access 1000 genome data Anna Scott
- Annotating variants annovar/snpeff/plink/vaast/qiime Dhivya & Scott shell/perl/python scripting – candidates for recessive disease
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