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 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.
Download
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