Genetic ancestry estimation software tools | Population genetics data analysis
The estimation of genetic ancestry in human populations has important applications in medical genetic studies. Genetic ancestry is used to control for population stratification in genetic association studies, and is used to understand the genetic basis for ethnic differences in disease susceptibility.
Investigates single nucleotide polymorphism (SNP) data. DIYABC is based on a simulation algorithm allowing the treatment of multi-population datasets with large number of loci. It can take into account complex population histories including any combination of population divergence events, admixture events and changes in past population size. This tool can serve to compare competing evolutionary scenarios and quantify their relative support.
Supports formal tests of whether admixture occurred. AdmixTools is a suite of methods for learning about population mixtures. This package infers admixture proportions and dates. It implements five methods: the three-population test, D-statistics, F4-ratio estimation, admixture graph fitting, and rolloff. It also computes lower and upper bounds on each admixture proportion.
A powerful discriminative modeling approach that is faster (~30x) and more accurate than existing methods. We accomplish this by using a conditional random field parameterized by random forests trained on reference panels. RFMix is capable of learning from the admixed samples themselves to boost performance and autocorrect phasing errors. RFMix shows high sensitivity and specificity in simulated Hispanics/Latinos and African Americans and admixed Europeans, Africans, and Asians.