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| == Introduction == | | == Introduction == |
| + | Main Workshop wiki page: [[SeqShop: December 2014]] |
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| 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. |
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| 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. |
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− | 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]. |
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| == 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]] |
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| + | == HGDP reference panel == |
| + | [[File:HGDP Popualtions.png|thumb|center|alt=HGDP populations |400px|HGDP populations]] |
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| == Setup in person at the SeqShop Workshop == | | == Setup in person at the SeqShop Workshop == |
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| + | <div class="mw-collapsible mw-collapsed" style="width:600px"> |
| + | ''If you are not already logged in, please expand this section.'' |
| + | <div class="mw-collapsible-content"> |
| {{SeqShopLogin}} | | {{SeqShopLogin}} |
| + | </div> |
| + | </div> |
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| === Setup your run environment=== | | === Setup your run environment=== |
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| 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 |
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| What is in the setup.txt file: | | What is in the setup.txt file: |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | 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 |
| </div> | | </div> |
| </div> | | </div> |
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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> |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | :<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> |
| </div> | | </div> |
| </div> | | </div> |
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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> |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | :<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> |
| </div> | | </div> |
| </div> | | </div> |
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| Create a working directory: | | Create a working directory: |
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− | mkdir $OUT/ancestry | + | mkdir -p $OUT/ancestry |
| cd $OUT/ancestry | | cd $OUT/ancestry |
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| Download and decompress software package: | | Download and decompress software package: |
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− | 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 |
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| == Preparing input files for LASER == | | == Preparing input files for LASER == |
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| 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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− | <div class="mw-collapsible mw-collapsed" style="width:500px"> | + | <div class="mw-collapsible" style="width:500px"> |
| In person at workshop notes: | | In person at workshop notes: |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| </div> | | </div> |
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− | <div class="mw-collapsible" style="width:500px"> | + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| Outside of the workshop notes: | | Outside of the workshop notes: |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| 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: |
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− | cp -r ./LASER-2.01/plot/ ./ | + | cp -r $LASER/plot/ ./ |
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| Go to the plot folder and run the script to plot results: | | Go to the plot folder and run the script to plot results: |
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| 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]] |
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| + | == Return to Workshop Wiki Page == |
| + | Return to main workshop wiki page: [[SeqShop: December 2014]] |