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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:

###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.

###Multiplicity of Infection:

Fws - using my Rmd Fws script to decide monoclonal vs multiclonal.
estMoi - using this perl script to calculate an actual MOI for each of my Pv and Pf samples.
pvmsp1 deep sequencing - Deen deep sequenced all these to get a sense of MOI. Want to see how well it agrees with Fws and estMoi.

###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 - Using primarily LUMPY.
mal10mal13 - Jess suggested that we look to see if these mutations, described in Michele's Lancet ID paper, correlate with CP group.

###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.
selscan - This does iHS, EHH, XP-EHH, and something even newer. What I'm going to try to use for looking at selection.
rehh - This is what Andrew used to make bifurcation diagrams for EHH stats.
Identity by Descent - A related question to selective sweeps is identity by descent - finding genomic fragments that are shared among samples.

###Cool Images:

circos - Cool, perl-based circular image maker. But I actually ended up using circlize in R.

###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.
characterizeCoverage - Use bedtools to determine percent of genes covered to a certain depth.
resistanceSNPs - Want to determine the frequency of variants in resistance genes for Pv and Pf.
exonuclease - Exploring association between CP groups and Chr 13 Exo 415 mutation.