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Day 2: Mapping & Variants
• 30 minutes: mapped data evaluation with samtools
• 30 min Installing/compiling tools: (aside from “module”) JB’s tool – google code Jeff
• 45 min View output & compare: false pos/neg – comparisons; what’s hard & weird - in IGV (GVF file/VCF file/BAMs). Jeff Geoff will check vcftools; also assess freebayes (Geoff) @GRC: bedtools will be needed to compare.
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• 30 min UCSC genome browser, GEO/SRA data downloads Anna
• 30 min 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
• 60 min Characterizing & comparing variant files – annovar/snpeff/plink/vaast/qiime Dhivya & Scott shell/perl/python scripting – candidates for recessive disease
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