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SeqShop: Estimates of Genetic Ancestry Practical, June 2014 (view source)

Revision as of 13:57, 3 July 2014

1,733 bytes added ,  13:57, 3 July 2014
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[[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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{{SeqShopLogin}}
     −
== Getting started ==
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== Setup in person at the SeqShop Workshop ==
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Create a working directory:
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''This section is specifically for the SeqShop Workshop computers.''
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<div class="mw-collapsible mw-collapsed" style="width:600px">
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''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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mkdir ancestry
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cd ancestry
     −
Download and decompress software package:
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{{SeqShopLogin}}
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wget http://www.sph.umich.edu/csg/chaolong/LASER/LASER-2.01.tar.gz
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=== Setup your run environment===
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tar xzvf LASER-2.01.tar.gz
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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.
   −
Set up to access data:
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This will setup some environment variables to point you to
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* Tutorial input files
 
  source /home/chaolong/LASER-Tutorial/setup.txt
 
  source /home/chaolong/LASER-Tutorial/setup.txt
 +
* 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">
 
What is in the setup.txt file:
 
What is in the setup.txt file:
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<div class="mw-collapsible-content">
 
  export GC=/home/mktrost/seqshop/gotcloud
 
  export GC=/home/mktrost/seqshop/gotcloud
 
  export REF=/home/mktrost/seqshop/reference/all
 
  export REF=/home/mktrost/seqshop/reference/all
 
  export HGDP=/home/chaolong/LASER-Tutorial/HGDP
 
  export HGDP=/home/chaolong/LASER-Tutorial/HGDP
 
  export BAM=/home/chaolong/LASER-Tutorial/BAM
 
  export BAM=/home/chaolong/LASER-Tutorial/BAM
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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>
 +
    
== Setup when running on your own outside of the SeqShop Workshop ==
 
== Setup when running on your own outside of the SeqShop Workshop ==
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<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 
=== Download the example data ===
 
=== Download the example data ===
 +
    
=== Setup your run environment ===
 
=== Setup your run environment ===
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* Point to where you want the output to go
 
* Point to where you want the output to go
 
*:<pre>export OUT=/home/username/seqshop_output/</pre>
 
*:<pre>export OUT=/home/username/seqshop_output/</pre>
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* Additional variables for Ancestry:
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*:<pre>export REF=$SS/ancestry/ref&#10;export HGDP=$SS/ancestry/HGDP&#10;export BAM=$SS/ancestry/bams</pre>
 
</div>
 
</div>
 
</div>
 
</div>
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* Point to where you want the output to go
 
* Point to where you want the output to go
 
*:<pre>setenv OUT /home/username/seqshop_output/</pre>
 
*:<pre>setenv OUT /home/username/seqshop_output/</pre>
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* Additional variables for Ancestry:
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*:<pre>setenv REF $SS/ancestry/ref&#10;setenv HGDP $SS/ancestry/HGDP&#10;setenv BAM $SS/ancestry/bams</pre>
 
</div>
 
</div>
 
</div>
 
</div>
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</div>
 
</div>
 
</div>
 
</div>
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 +
 +
== Getting started ==
 +
Create a working directory:
 +
 +
mkdir $OUT/ancestry
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cd $OUT/ancestry
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 +
Download and decompress software package:
 +
 +
wget http://www.sph.umich.edu/csg/chaolong/LASER/LASER-2.01.tar.gz
 +
tar xzvf LASER-2.01.tar.gz
 +
    
== 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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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.
     −
   $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101035.recal.bam > $OUT/121101035.recal.pileup &
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<div class="mw-collapsible mw-collapsed" style="width:500px">
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  # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101043.recal.bam > $OUT/121101043.recal.pileup &  
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In person at workshop notes:
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  # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101050.recal.bam > $OUT/121101050.recal.pileup &
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<div class="mw-collapsible-content">
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  # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101052.recal.bam > $OUT/121101052.recal.pileup &
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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.
−
  # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101415.recal.bam > $OUT/121101415.recal.pileup &
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*It takes about 2 mins for each pileup job.
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  # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101861.recal.bam > $OUT/121101861.recal.pileup &
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</div>
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</div>
 +
 
 +
<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.
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*Pileup files for the whole genome BAMs are provided with the download and will be used in the next step.
 +
</div>
 +
</div>
 +
 
 +
   $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/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/121101052.recal.bam > 121101052.recal.pileup &
 +
  # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101415.recal.bam > 121101415.recal.pileup &
 +
  # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101861.recal.bam > 121101861.recal.pileup &
    
We use -q 30 and -Q 20 to exclude reads that have mapping quality score lower than 30 or base quality score lower than 20.
 
We use -q 30 and -Q 20 to exclude reads that have mapping quality score lower than 30 or base quality score lower than 20.
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In this step, we will generate a file called "hapmap_trios.seq", containing the information of 6 samples. It takes about 30 seconds to run.
 
In this step, we will generate a file called "hapmap_trios.seq", containing the information of 6 samples. It takes about 30 seconds to run.
 
We will use the pre-generated pileup files in the $BAM folder.
 
We will use the pre-generated pileup files in the $BAM folder.
 +
* These pre-generated pileup files are for the whole genome of all 6 samples
    
  python ./LASER-2.01/pileup2seq/pileup2seq.py \
 
  python ./LASER-2.01/pileup2seq/pileup2seq.py \
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11130"

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