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SeqShop: Estimates of Genetic Ancestry Practical, May 2015 (view source)

Revision as of 09:57, 2 February 2017

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→‎Introduction
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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].
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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 ==
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[[File:HGDP Popualtions.png|thumb|center|alt=HGDP populations |400px|HGDP populations]]
 
[[File:HGDP Popualtions.png|thumb|center|alt=HGDP populations |400px|HGDP populations]]
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== Setup in person at the SeqShop Workshop ==
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== Setup ==
 
''This section is specifically for the SeqShop Workshop computers.''
 
''This section is specifically for the SeqShop Workshop computers.''
 
<div class="mw-collapsible mw-collapsed" style="width:600px">
 
<div class="mw-collapsible mw-collapsed" style="width:600px">
 
''If you are not running during the SeqShop Workshop, please skip this section.''
 
''If you are not running during the SeqShop Workshop, please skip this section.''
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<div class="mw-collapsible-content">
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<div class="mw-collapsible mw-collapsed" style="width:600px">
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''If you are not already logged in, please expand this section.''
   
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 
{{SeqShopLogin}}
 
{{SeqShopLogin}}
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</div>
 
</div>
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=== Setup your run environment===
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This is the same setup you did for the previous tutorial, but you need to redo it each time you log in.
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This will setup some environment variables to point you to
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* Tutorial input files
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source /net/seqshop-server/home/chaolong/LASER-Tutorial/setup.txt
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* You won't see any output after running <code>source</code>
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** It silently sets up your environment
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<div class="mw-collapsible mw-collapsed" style="width:400px">
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What is in the setup.txt file:
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<div class="mw-collapsible-content">
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export GC=/net/seqshop-server/home/mktrost/seqshop/gotcloud
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export REF=/net/seqshop-server/home/mktrost/seqshop/gotcloud/gotcloud.ref
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export HGDP=/net/seqshop-server/home/chaolong/LASER-Tutorial/HGDP
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export BAM=/net/seqshop-server/home/chaolong/LASER-Tutorial/BAM
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export LASER=/net/seqshop-server/home/chaolong/LASER-Tutorial/LASER-2.01
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</div>
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</div>
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Point to where you want the output to go replacing the path with where you would like your output to go
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<pre>export OUT=~/seqshop_output/</pre>
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</div>
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</div>
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== Setup when running on your own outside of the SeqShop Workshop ==
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''This section is specifically for running on your own outside of the SeqShop Workshop.''
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<div class="mw-collapsible" style="width:600px">
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''If you are running during the SeqShop Workshop, please skip this section.''
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<div class="mw-collapsible-content">
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=== Prerequisite Tutorials ===
 
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#Setup_when_running_on_your_own_outside_of_the_SeqShop_Workshop|Tutorial Setup]]
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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
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  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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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" style="width:500px">
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In person at workshop notes:
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<div class="mw-collapsible-content">
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*Please only try one sample so that we won't overload the sever with everyone running 6 jobs at the same time. Pileup files for these 6 samples have been prepared for later steps.
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*It takes about 2 mins for each pileup job.
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</div>
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</div>
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<div class="mw-collapsible mw-collapsed" style="width:500px">
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Outside of the workshop notes:
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<div class="mw-collapsible-content">
   
*The BAMs provided as part of the download are chr22 only BAMs.  They are used to demonstrate how to run this step.
 
*The BAMs provided as part of the download are chr22 only BAMs.  They are used to demonstrate how to run this step.
 
*Pileup files for the whole genome BAMs are provided with the download and will be used in the next step.
 
*Pileup files for the whole genome BAMs are provided with the download and will be used in the next step.
 
* You only need to try one of these.
 
* You only need to try one of these.
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</div>
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</div>
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  $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101035.recal.bam > 121101035.recal.pileup
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# $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101035.recal.bam > 121101035.recal.pileup
 
  # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101043.recal.bam > 121101043.recal.pileup  
 
  # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101043.recal.bam > 121101043.recal.pileup  
 
  # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101050.recal.bam > 121101050.recal.pileup
 
  # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101050.recal.bam > 121101050.recal.pileup
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== FEEDBACK! ==
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Sorry, I forgot to ask for feedback yesterday, so please fill out the survey for yesterday if you have not already done so:
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https://docs.google.com/forms/d/1xLrrEJ3XeZjxR_e5Fo-OTKHQvUFQLgX8MYwLZtxroig/viewform
    
== Return to Workshop Wiki Page ==
 
== Return to Workshop Wiki Page ==
 
Return to main workshop wiki page: [[SeqShop: May 2015]]
 
Return to main workshop wiki page: [[SeqShop: May 2015]]
Ppwhite
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