Analysis | Basis | Reference |
---|---|---|
Contamination estimates based on the X-chromosomes | BC | [19] b |
Type specific error estimation estimated by simultaneously estimating allele frequencies and genotype likelihoods | GL | [10] |
Type specific error estimation based on an outgroup and a high quality genome | BC | [20] ab |
Genotype likelihoods (GL) (diploids) | BC/Seq | |
Allele frequencies for a site | BC/GL/GP | |
SNP discovery (LRT) used for rejecting that the allele frequency is different from zero | GL | [10] |
Genotype posteriors (GP) can be used for calling genotypes by specifying a cutoff | GL/SAF | |
Sample allele frequencies (SAF) the probability of all read data given the sample allele frequency | GL/GP | [9] b |
Population differentiation statistics F st | SAF | [14] ac |
Population structure via principle components analysis (PCA) | GP | [14] ac |
Admixture analysis (NGSadmix) NGS data | GL | [22] ab |
Detection of ancient admixture ABBA-BABA/d-statistics | BC | [20] b |
Estimation of SFS (1D) | SAF | [9] ab |
Estimation of SFS (2D) | SAF | Â |
Selection scans, Neutrality tests (e.g θ's and Tajima's D) | SAF | [12] ab |
Estimation of individual and site-wise Inbreeding coefficients. Also MAF and GP estimation for inbreed individuals | GL | [13] abc |
Allele frequency based association for case/control data) | GL | [10] |
Association score test in a generalized linear model framework for both quantitative and case/control data while allowing for additional covariates | GL-GP | [11] b |