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Welcome to the cambodiaWGS wiki!

I will document my analysis through this wiki. The associated scripts (and results?) will be kept in this repo.

###Steps to good SNP-call data:

• variantCalling - documented as part of the gatk_pipeline repo.
• weakestLinks - remove the lowest-coverage samples prior to downstream analysis. Gives us a shot at getting full haplotypes for all SNPs.
• variantFiltering - modeled loosely after Manske et al.

###Population Differentiation:

• vcf2structure - VCF file format must be converted to STRUCTURE format for both STRUCTURE and adegenet analysis.
• structure
• adegenet
• recombination
• Derrick's dupFinder