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Revision as of 10:24, 2 February 2017
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== Introduction ==
== Introduction ==
Main Workshop wiki page: [[SeqShop: December 2014]]
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 ==
[[File:LASER-workflow.png|thumb|center|alt=LASER workflow|400px|LASER workflow]]
[[File:LASER-workflow.png|thumb|center|alt=LASER workflow|400px|LASER workflow]]
== HGDP reference panel ==
[[File:HGDP Popualtions.png|thumb|center|alt=HGDP populations |400px|HGDP populations]]
== Setup in person at the SeqShop Workshop ==
== Setup in person at the SeqShop Workshop ==
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''If you are not already logged in, please expand this section.''
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{{SeqShopLogin}}
{{SeqShopLogin}}
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=== Setup your run environment===
=== Setup your run environment===
This will setup some environment variables to point you to
This will setup some environment variables to point you to
* Tutorial input files
* Tutorial input files
source /home/chaolong/LASER-Tutorial/setup.txt
source /net/seqshop-server/home/chaolong/LASER-Tutorial/setup.txt
* You won't see any output after running <code>source</code>
* You won't see any output after running <code>source</code>
** It silently sets up your environment
** It silently sets up your environment
What is in the setup.txt file:
What is in the setup.txt file:
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export GC=/home/mktrost/seqshop/gotcloud
export GC=/net/seqshop-server/home/mktrost/seqshop/gotcloud
export REF=/home/mktrost/seqshop/gotcloud/gotcloud.ref
export REF=/net/seqshop-server/home/mktrost/seqshop/gotcloud/gotcloud.ref
export HGDP=/home/chaolong/LASER-Tutorial/HGDP
export HGDP=/net/seqshop-server/home/chaolong/LASER-Tutorial/HGDP
export BAM=/home/chaolong/LASER-Tutorial/BAM
export BAM=/net/seqshop-server/home/chaolong/LASER-Tutorial/BAM
export LASER=/home/chaolong/LASER-Tutorial/LASER-2.01
export LASER=/net/seqshop-server/home/chaolong/LASER-Tutorial/LASER-2.01
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<li>Using bash (replace the paths below with the appropriate paths):</li>
<li>Using bash (replace the paths below with the appropriate paths):</li>
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:<pre>export REF=$SS/ancestry/ref export HGDP=$SS/ancestry/HGDP export BAM=$SS/ancestry/bams</pre>
:<pre>export LASER=$OUT/ancestry/LASER-2.01 export REF=$SS/ancestry/ref export HGDP=$SS/ancestry/HGDP export BAM=$SS/ancestry/BAM</pre>
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<li>Using tcsh (replace the paths below with the appropriate paths):</li>
<li>Using tcsh (replace the paths below with the appropriate paths):</li>
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:<pre>setenv REF $SS/ancestry/ref setenv HGDP $SS/ancestry/HGDP setenv BAM $SS/ancestry/bams</pre>
:<pre>setenv LASER $OUT/ancestry/LASER-2.01 setenv REF $SS/ancestry/ref setenv HGDP $SS/ancestry/HGDP setenv BAM $SS/ancestry/BAM</pre>
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Create a working directory:
Create a working directory:
mkdir $OUT/ancestry
mkdir -p $OUT/ancestry
cd $OUT/ancestry
cd $OUT/ancestry
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 ==
This step uses samtools to generate pileup files from bam files.
This step uses samtools to generate pileup files from bam files.
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In person at workshop notes:
In person at workshop notes:
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Outside of the workshop notes:
Outside of the workshop notes:
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LASER can perform principal components analysis (PCA) on genotype data of the reference panel to generate a reference ancestry space.
LASER can perform principal components analysis (PCA) on genotype data of the reference panel to generate a reference ancestry space.
# ./LASER-2.01/laser -g $HGDP/HGDP_938.geno -pca 1 -k 30 -o HGDP_938
# $LASER/laser -g $HGDP/HGDP_938.geno -pca 1 -k 30 -o HGDP_938
The above command takes ~20 minutes to finish.
The above command takes ~20 minutes to finish.
Submit two jobs to place sequenced samples into the reference ancestry space:
Submit two jobs to place sequenced samples into the reference ancestry space:
$LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 1 -y 3 -o hapmap_trios.1-3 &
$LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 4 -y 6 -o hapmap_trios.4-6 &
The first job will process samples 1 to 3 and the second job will processed samples 4 to 6.
The first job will process samples 1 to 3 and the second job will processed samples 4 to 6.
Example R codes are available in ./LASER-2.01/plot/. Let's copy the folder to current working directory:
Example R codes are available in ./LASER-2.01/plot/. Let's copy the folder to current working directory:
cp -r ./LASER-2.01/plot/ ./
cp -r $LASER/plot/ ./
Go to the plot folder and run the script to plot results:
Go to the plot folder and run the script to plot results:
We expect to see the following figure, in which 3 CEU samples cluster with HGDP Europeans and 3 YRI samples cluster with HGDP Africans:
We expect to see the following figure, in which 3 CEU samples cluster with HGDP Europeans and 3 YRI samples cluster with HGDP Africans:
[[File:Results_on_HGDP.png|thumb|center|alt=LASER results|400px|LASER results]]
[[File:Results_on_HGDP.png|thumb|center|alt=LASER results|400px|LASER results]]
== Return to Workshop Wiki Page ==
Return to main workshop wiki page: [[SeqShop: December 2014]]
