SEQMIX
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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 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.
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Related Programs
Local ancestry inference with high density genotype array data can be done with existing software HAPMIX, LAMP, ANCESTRYMAP.
Whole genome ancestry inference with ultra low coverage sequence data can be analyzed with LASER.
