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SeqShop: Estimates of Genetic Ancestry Practical, May 2015

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[[File:HGDP Popualtions.png|thumb|center|alt=HGDP populations |400px|HGDP populations]]
== Setup in person at the SeqShop Workshop ==
''This section is specifically for the SeqShop Workshop computers.''
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''If you are not running during the SeqShop Workshop, please skip this section.''
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''If you are not already logged in, please expand this section.''
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{{SeqShopLogin}}
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=== Setup your run environment===
This is the same setup you did for the previous tutorial, but you need to redo it each time you log in.
 
This will setup some environment variables to point you to
* Tutorial input files
source /net/seqshop-server/home/chaolong/LASER-Tutorial/setup.txt
* You won't see any output after running <code>source</code>
** It silently sets up your environment
 
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What is in the setup.txt file:
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export GC=/net/seqshop-server/home/mktrost/seqshop/gotcloud
export REF=/net/seqshop-server/home/mktrost/seqshop/gotcloud/gotcloud.ref
export HGDP=/net/seqshop-server/home/chaolong/LASER-Tutorial/HGDP
export BAM=/net/seqshop-server/home/chaolong/LASER-Tutorial/BAM
export LASER=/net/seqshop-server/home/chaolong/LASER-Tutorial/LASER-2.01
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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
<pre>export OUT=~/seqshop_output/</pre>
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== Setup when running on your own outside of the SeqShop Workshop ==
''This section is specifically for running on your own outside of the SeqShop Workshop.''
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''If you are running during the SeqShop Workshop, please skip this section.''
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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]]
Download and decompress software package:
wget http://wwwcsg.sph.umich.edu/csg/chaolong/LASER/LASER-2.01.tar.gz
tar xzvf LASER-2.01.tar.gz
This step uses samtools to generate pileup files from bam files.
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In person at workshop notes:
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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.
*It takes about 2 mins for each pileup job.
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Outside of the workshop notes:
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*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.
* You only need to try one of these.
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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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