Difference between revisions of "SEQMIX"

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(Related Programs)
(Method)
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== Method ==
 
== 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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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.
  
 
== Download ==
 
== Download ==

Revision as of 14:14, 13 March 2013

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.

Download

(Coming soon)

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.