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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.

###Getting Additional Populations:

• getting otherPops

###Steps to good SNP-call data:

• HaplotypeCaller - decided that I should look into GATK's HaplotypeCaller
• genomeCoverage - using bedtools and/or GATK's DepthOfCoverage.
• variantCalling - documented as part of the gatk_pipeline repo and the HaplotypeCaller updates are documented here.
• 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.
• [characterizeCoverage]

###Population Differentiation:

• PopGenome - the "Swiss Army Knife" package for population genetic analyses.
• vcf2structure - VCF file format must be converted to STRUCTURE format for both STRUCTURE and adegenet analysis.
• structure
• adegenet - this is for PCA in R
• recombination
• Derrick's dupFinder
• Structural Variant Analysis

###Selective Sweeps:

• hapFLK - Andrew found this and recommended. Looks like it is sensitive and specific for sweeps even in complicated demographic backgrounds, because it makes extended haplotypes, then does Fst on those, somehow.

###Cool Images:

• circos - Cool, perl-based circular image maker.

###Bottlenecks:

• Loss of Rare Alleles - If we find a greater loss of rare alleles in P. falciparum than in P. vivax, then maybe that's evidence that P. falciparum has undergone a greater genetic bottleneck than P. vivax.

###Demography

• dadi - Inference of population demographic parameters. What Hartl used in their MBE paper.

###Miscellaneous

• snpEff - Use it to predict SNP functions. Will be useful for subsetting variants for class analysis.