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Revision as of 10:23, 2 February 2017
, 10:23, 2 February 2017→Getting started
'''Note:''' the latest version of this practical is available at: [[SeqShop: Estimates of Genetic Ancestry Practical]]
* The ones here is the original one from the June workshop (updated to be run from elsewhere)
== Introduction ==
== Introduction ==
See the [[Media:LASER-tutorial.pdf|tutorial slides]] for an introduction of the LASER analysis workflow, input/output file formats, and usage of the LASER software.
See the [[Media:LASER-tutorial.pdf|tutorial slides]] for an introduction of the LASER analysis workflow, input/output file formats, and usage of the LASER software.
The main purpose of this page is to provide step-by-step command lines for using LASER to estimate ancestry of 6 targeted sequenced samples (2 HapMap trios) in a principal component space generated using genome-wide SNP data from the Human Genome Diversity Project (HGDP). The HGDP reference panel contains genotype data across 632,958 autosomal loci for 938 individuals from 53 populations worldwide.
The main purpose of this page is to provide step-by-step command lines for using LASER to estimate ancestry of 6 targeted sequenced samples (2 HapMap trios) in a principal component space generated using genome-wide SNP data from the Human Genome Diversity Project (HGDP). The HGDP reference panel contains genotype data across 632,958 autosomal loci for 938 individuals from 53 populations worldwide.
For more details about the options and usage of LASER, please read the [http://www.sph.umich.edu/csg/chaolong/LASER/LASER_Manual.pdf manual].
For more details about the options and usage of LASER, please read the [http://csg.sph.umich.edu//chaolong/LASER/LASER_Manual.pdf manual].
== LASER workflow ==
== LASER workflow ==
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
This tutorial uses samtools from GotCloud, as well as example data downloaded in the Sequence Mapping & Assembly tutorial, so if you have not already installed GotCloud and the tutorial data in a previous tutorial, please do so now: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#Setup_when_running_on_your_own_outside_of_the_SeqShop_Workshop|Tutorial Setup]]
This tutorial uses samtools from GotCloud, as well as example data downloaded in the Sequence Mapping & Assembly tutorial, so if you have not already installed GotCloud and the tutorial data in a previous tutorial, please do so now: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical, June 2014#Setup_when_running_on_your_own_outside_of_the_SeqShop_Workshop|Tutorial Setup]]
Download and decompress software package:
Download and decompress software package:
wget http://www.sph.umich.edu/csg/chaolong/LASER/LASER-2.01.tar.gz
wget http://csg.sph.umich.edu//chaolong/LASER/LASER-2.01.tar.gz
tar xzvf LASER-2.01.tar.gz
tar xzvf LASER-2.01.tar.gz
== Preparing input files for LASER ==
== Preparing input files for LASER ==
less -S hapmap_trios.SeqPC.coord
less -S hapmap_trios.SeqPC.coord
The results should look like below:
The results should look like below (results will vary slightly):
popID indivID L1 Ci K t PC1 PC2 PC3 PC4
popID indivID L1 Ci K t PC1 PC2 PC3 PC4
