Inferring the ancestry at each locus in the genome of recently admixed individuals (e.g. Latino Americans) plays a major role in medical and population genetic inferences ranging from finding disease risk loci to inferring recombination rates to mapping missing contigs in the human genome. Here we present a method that uses continental-specific variants (i.e. variants present in individuals from only one continental group such as Europeans or Africans) for accurate local ancestry inference.
Lanc-CSV is described here: Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals, Brown&Pasaniuc, PLoS Computational Biology 2014.
Beta version of the software package can be downloaded here: c++ and matlab version. We recommend using the c++ version (README); reference panels from 1000 Genomes phase 3 data for use with c++ version can be downloaded here.
Local ancestry calls for the 1000 Genomes admixed individuals using Lanc-CSV can be found here.