Changes

== Overview ==

== Overview ==

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

'''SEQMIX''' is a C++ program that takes advantage of off-targeted sequence reads from exome/targeted sequencing experiments for accurate local ancestry inference. The paper is currently accepted by AJHG and will appear at the November issue (link coming soon).

== Method ==

== Method ==

== Download ==

== Download ==

Here is a tar ball [[Media:SEQMIX_0.1.tar]] which compresses the following three folders

Here is a tar ball [[Media:SEQMIX_0.1.tar]] for SEQMIX (version 0.1) which compresses the following three folders

* libsrc: a folder contains source code from code written by Goncalo

* libsrc: a folder contains source code from code written by Goncalo Abecasis

* src: source code for SEQMIX

* src: source code for SEQMIX

* Release: example files and command as well as the Readme.txt file that explains how to run SEQMIX

* Release: example files and command file as well as the Readme.txt file that explains how to run SEQMIX

Before you run SEQMIX, or even while you are running SEQMIX examples (summarized by the example.sh file), please refer to the Readme.txt file for detailed explanation of the two steps for running SEQMIX.  

Before you run SEQMIX, or even while you are running SEQMIX examples (summarized by the '''example.sh''' file), please refer to the '''Readme.txt''' file for detailed explanations of the two steps for running SEQMIX.  

Note that SEQMIX requires these specified files

Note that SEQMIX requires these specified files

* allele frequency for Africans

* allele frequency for Africans

* allele frequency for European

* allele frequency for Europeans

* genetic distance file  

* genetic distance file  

* input vcf  

* input vcf  

The input vcf file is generated from sequencing experiment and the downstream data processing steps. The allele frequency and genetic distance files should be prepared by users and sometimes are tedious to do. The good news is that I have used these files for the whole genome level. Please contact me (youna@umich.edu) if you would like to use it. I will point you to the path if you are internal user and will figure out a way to share them (These files are fairly big) if you are a external users.

The input vcf file is generated from sequencing experiment and the downstream data processing steps. The allele frequency and genetic distance files should be prepared by users and sometimes are tedious to do. The good news is that I have used these files for the whole genome level. Please contact me (''youna@umich.edu'') if you would like to have them. I will point you to the path if you are internal user and will figure out a way to share them (These files are fairly big) if you are a external users.

 

 

Please contact Youna Hu (''youna@umich.edu'') if you have any questions or suggestions for SEQMIX.

== Related Programs ==

== Related Programs ==