LAI_benchmarking

scripts for benchmarking local ancestry

Data sources

Reference Data

taken from 1000G YRI,CEU,PEL, and MXL

Genetic maps

used 1000G genetic maps interolated with the genetic maps generated by the HapMap 2 Project sourced from this github https://github.com/joepickrell/1000-genomes-genetic-maps

Software Sources

RFMix v1.54 LAMPLD MOSAIC ELAI Loter admixture simulation tool

Dependencies

Pandas Numpy bcftools vcftools Other dependencies required for software install (please see individual software installation)