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= Introduction =
= Introduction =
LASER, which stands for Locating Ancestry using SEquencing Reads, is a C++ software package that can estimate individual ancestry directly from genome-wide shortgun sequencing reads without calling genotypes. The method relies on the availability of a set of reference individuals whose genome-wide SNP genotypes and ancestral information are known. We first construct a reference coordinate system by applying principal components analysis (PCA) to the genotype data of the reference individuals. Then, for each sequencing sample, use the genome-wide sequencing reads to place the sample into the reference PCA space. With an appropriate reference panel, the estimated coordinates of the sequencing samples identify their ancestral background and can be directly used to correct for population structure in association studies or to ensure adequate matching of cases and controls.
LASER, which stands for Locating Ancestry using SEquencing Reads, is a C++ software package that can estimate individual ancestry directly from genome-wide shortgun sequencing reads without calling genotypes. The method relies on the availability of a set of reference individuals whose genome-wide SNP genotypes and ancestral information are known. We first construct a reference coordinate system by applying principal components analysis (PCA) to the genotype data of the reference individuals. Then, for each sequencing sample, use the genome-wide sequencing reads to place the sample into the reference PCA space. With an appropriate reference panel, the estimated coordinates of the sequencing samples identify their ancestral background and can be directly used to correct for population structure in association studies or to ensure adequate matching of cases and controls.
The goal of this wiki page is to help you get start using LASER, and we encourage you to read the [http://www.sph.umich.edu/csg/chaolong/LASER/LASER_Manual.pdf manual] for more details.
Note:
The goal of this wiki page is to help you get start using LASER.
This page was created for LASER 1.0. Some of the information might be outdated for LASER 2.0.
A more updated wiki page can be found at [http://genome.sph.umich.edu/wiki/SeqShop:_Estimates_of_Genetic_Ancestry_Practical 2014 UM Sequencing Workshop].
We also encourage you to read the [http://csg.sph.umich.edu/chaolong/LASER/LASER_Manual.pdf manual] for more details of the software.
= Download =
= Download =
To get a copy of the software and manual, go to the [http://www.sph.umich.edu/csg/chaolong/LASER/ LASER Download] page.
To get a copy of the software and manual, go to the [http://csg.sph.umich.edu//chaolong/LASER/ LASER Download] page.
= Workflow =
= Workflow =
LASER has advanced options including (1) parallel computing; (2) increase ancestry inference accuracy using repeated runs; (3) generate PCA coordiates using genotypes.
LASER has advanced options including (1) parallel computing; (2) increase ancestry inference accuracy using repeated runs; (3) generate PCA coordiates using genotypes.
See [http://www.sph.umich.edu/csg/chaolong/LASER/LASER_Manual.pdf LASER Manual] for detailed information.
See [http://csg.sph.umich.edu//chaolong/LASER/LASER_Manual.pdf LASER Manual] for detailed information.
= Contact =
= Contact =
