Pipeline for infering local ancestry without phased data by using ELAI
The software is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. In no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the software or the use or other dealings in the software.
Also see ELAI documentation http://www.haplotype.org/download/elai-manual.pdf
ELAI: http://www.haplotype.org/elai.html Vcftools: https://vcftools.github.io/man_latest.html
Inference of the local ancestry with ELAI
Determination of the haplotypes length and number. Computation of the Chromosomal Ancestry Imbalance
Estimation of the genome-wide introgression rate