SEQMIX

Overview

SEQMIX is a C++ program that takes advantage of off-targeted sequence reads from exome/targeted sequencing experiments for accurate local ancestry inference.

Method

Before running SEQMIX, it is important to pre-process your data with a LD pruning step, which identify sites that are in high LD (r^2 > 0.1) and keep the sites with a higher sequence depth into the model. Since the sequence depth distribution is sample dependent, it is necessary to prune the sequence data for each individual.

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Related Programs

Local ancestry inference with high density genotype array data can be done with existing software HAPMIX, LAMP, ANCESTRYMAP. (Warning: These programs are not user friendly and are very difficult to get it running)

Whole genome ancestry inference with ultra low coverage sequence data can be analyzed with LASER.