SEQMIX is a C++ program that takes advantage of off-targeted sequence reads from exome/targeted sequencing experiments for accurate local ancestry inference.
Before running SEQMIX, it is important to LD prune your data so that pairs of sites in high LD (r^2 > 0.1) are identified and only the one with a higher sequence depth are included into the model. As the sequence depth distribution is sample dependent, it is necessary to prune the sequence data for each individual.
Here is a tar ball Media:SEQMIX_0.1.tar which compresses the following three folders
- libsrc: a folder contains source code from code written by Goncalo
- src: source code for SEQMIX
- Release: example files and command as well as the Readme.txt file that explains how to run SEQMIX
Whole genome ancestry inference with ultra low coverage sequence data can be analyzed with LASER.