Changes

From Genome Analysis Wiki
Jump to navigationJump to search

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

Revision as of 14:58, 19 May 2015

2,032 bytes removed ,  14:58, 19 May 2015
no edit summary
Line 15: Line 15:  
[[File:HGDP Popualtions.png|thumb|center|alt=HGDP populations |400px|HGDP populations]]
 
[[File:HGDP Popualtions.png|thumb|center|alt=HGDP populations |400px|HGDP populations]]
   −
== Setup in person at the SeqShop Workshop ==
+
== 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.''
−
<div class="mw-collapsible-content">
  −
  −
  −
<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">
 
<div class="mw-collapsible-content">
 
{{SeqShopLogin}}
 
{{SeqShopLogin}}
Line 29: Line 24:  
</div>
 
</div>
   −
=== 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
  −
  −
<div class="mw-collapsible mw-collapsed" style="width:400px">
  −
What is in the setup.txt file:
  −
<div class="mw-collapsible-content">
  −
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
  −
</div>
  −
</div>
  −
  −
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>
  −
</div>
  −
</div>
  −
  −
== 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.''
  −
<div class="mw-collapsible" style="width:600px">
  −
''If you are running during the SeqShop Workshop, please skip this section.''
  −
<div class="mw-collapsible-content">
      +
=== 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]]
   Line 93: Line 59:  
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
   Line 108: Line 74:  
This step uses samtools to generate pileup files from bam files.  
 
This step uses samtools to generate pileup files from bam files.  
   −
<div class="mw-collapsible" style="width:500px">
  −
In person at workshop notes:
  −
<div class="mw-collapsible-content">
  −
*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.
  −
</div>
  −
</div>
  −
  −
<div class="mw-collapsible mw-collapsed" style="width:500px">
  −
Outside of the workshop notes:
  −
<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.
−
</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/121101035.recal.bam > 121101035.recal.pileup
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13365"

Navigation menu